David Krejci, Tyler Seguin and Patrice Bergeron each scored for the Bruins. Thomas gave up goals to Matt Read and Claude Giroux, but stoned Danny Briere for the much-needed victory.
The Bruins snap their season-high four-game losing streak and jump back into first place in the Northeast Division, at least for now, pending the result of Ottawa's game against Toronto Saturday night.
The Bruins will face the Leafs as well on Monday when they try to carry the momentum of this win into their next game and start a streak in the opposite direction with a second victory in a row.
End Overtime, 2-2: This one will be settled in a shootout, with the Bruins' quest to end their losing streak coming down to a skills competition.
Overtime, 3:30, 2-2: The Bruins come even closer, with Chara clanging the near post with a shot from the left circle.
Overtime, 2:48, 2-2: The Bruins come close to winning this one, but Chris Kelly's tip in front goes wide.
Overtime, 0:00, 2-2: The five-minute extra session is under way. the sides will skate 4 on 4 in the sudden death OT, then head to a shootout if neither side can score.
End Regulation, 2-2: This one is headed to overtime. The Bruins salvage at least a point after surviving some strong Philadelphia pressure in the final minute, but they really need to take the extra point and come away with a win from this one.
Third Period, 17:30, 2-2: The Bruins show some life as they try to answer the Philly goal with some pressure of their own, but Bryzgalov stands strong to keep it tied.
Third Period, 15:43, 2-2: The Flyers pull even late with another deflection in front, this time by Jakub Voracek.
Braydon Coburn sent in the shot from the left point and Voracek tipped it in at the left slot.
Third Period, 13:04, Bruins 2-1: The Bruins come up with a huge penalty kill there. Gregory Campbell went down to block a blast, one of several key plays to maintain the lead before Thornton returns to the ice to put the sides back at even strength.
Third Period, 11:04, Bruins 2-1: The Bruins will be shorthanded as Shawn Thornton is called for goalie interference after making contact with Bryzgalov cutting through the crease.
Third Period, 10:30, Bruins 2-1: A dangerous whiff on a clear by Greg Zanon to the left of the Bruins goal, but Boston managed to clear the puck, albeit by icing it as the the faceoff comes back to the Bruins end.
Third Period, 6:50, Bruins 2-1: The Bruins creating chances now, first with Daniel Paille breaking in from the left wing for a bid, then with Tyler Seguin charging down the right wing. But Bryzgalov turned aside both shots to keep it a one-goal game.
Third Period, 3:53, Bruins 2-1: The Bruins had a 3 on 2 break become a 4 on 2 when Chara jumped up into the play, but Chara couldn't handle Caron's pass and the Bruins don't get a shot out of the opportunity.
Third Period, 1:39, Bruins 2-1: The Flyers have announced that defensemen Andreas Lilja and forward Max Talbot, both injured earlier in the game, will not return to this one.
Third Period, 0:00, Bruins 2-1: The final frame is under way here at the Garden, with the Bruins looking to close out the win, end their losing streak and retake first place in the division, at least until Ottawa plays Saturday night.
Second Intermission Notes: It was a much more even frame in the second. The Bruins generated chances early, but couldn't extend the lead, and Philadelphia finally broke through with a goal to cut it to 2-1 going to the third.
The Bruins will need to pick up their intensity in the third to close out what would be a huge win.
End Second Period, Bruins 2-1: The middle frame comes to a close, but not before the Flyers trim the Bruins' lead to a single goal. The Bruins will need a big effort in the third to close this one out and end their losing streak.
Second Period, 18:51, Bruins 2-1: Up and down action with both teams creating chances late in the period. This isn't the kind of wide-open play the Bruins want. They need to tighten up to take this lead into the third.
Second Period, 16:50, Bruins 2-1: Dennis Seidenberg, who nailed Wayne Simmonds with a big hit earlier, buries Scott Hartnell behind the net. Hartnell has been very quiet since his early confrontation with Chara in the opening period.
Second Period, 13:23, Bruins 2-1: The Bruins have done a good job of settling things down and keeping play in the Philly end since the goal, not giving the Flyers opportunities to build off that and pull even.
Second Period, 9:16, Bruins 2-1: The Bruins come within two seconds of killing that penalty off, but Matt Read puts Philadelphia on the board with a deflection in front just before the penalty expired.
Danny Briere sent the shot in and Read tipped it in the slot past Thomas to cut the Bruins lead in half.
Second Period, 7:17, Bruins 2-0: The Bruins will have an important penalty to kill off here to maintain the momentum and their two-goal lead as Tyler Seguin is sent to the box for slashing.
Second Period, 4:08, Bruins 2-0: The gloves come off again as Johnny Boychuk and Max Talbot engage in a quick scrap with Boychuk landing a couple rights to put Talbot down fast.
Second Period, 3:49, Bruins 2-0: The Bruins created some chances and kept the puck in the Philly zone for most of the power play, but couldn't cash in as the Flyers return to full strength.
Second Period, 1:49, Bruins 2-0: The Bruins have continued the pressure to start the second, and it resulted in scoring chances for both the Krejci line and Bergeron in front, the latter leading to a Zac Rinaldo hooking penalty as the Bruins go back on the power play.
Second Period, 0:00, Bruins 2-0: The middle frame is under way here at the Garden, where the Bruins are looking to build off a strong opening period and maintain the intensity they showed in the first for two more periods to put an end to their four-game losing streak.
First Intermission Notes: The Bruins finally came out strong to start a matinee and they have played with the kind of effort and intensity too often lacking in their recent outings.
The Bruins dominated just about every category in that frame. They outhit Philadelphia 12-3, with Shawn Thornton and Jordan Caron each collecting as many hits as the entire Flyers squad. The Bruins also were 15-9 on faceoffs, thanks to Chris Kelly (8-2) and Patrice Bergeron (5-2) and outshot the Flyers 11-7.
It took Philadelphia nearly half the period to put its first shot on Tim Thomas, who looks sharper than he's been in weeks. He made several big stops, including denying Jaromir Jagr on a breakaway after Jagr came out of the penalty box.
The Bruins have been playing from behind throughout their recent losing streak. Now they finally have a lead, but they must continue to press the attack and can't fall back into any bad habits in the final two periods.
End First Period, Bruins 2-0: The opening period has come to a close, and it was one of the best frames the Bruins have put together in some time. They were rewarded for their efforts with a two-goal lead, but will have to maintain this level of play for two more periods to put an end to their losing streak.
First Period, 17:07, Bruins 2-0: The Bruins double the lead as Tyler Seguin scores a huge one to make it 2-0.
Seguin put it home at the right post off a feed from behind the net by Patrice Bergeron.
First Period, 16:24, Bruins 1-0: The Bruins were stuck in their own zone for most of that power play, but they did a good job of limiting the chances Philadelphia had and are now back at full strength.
First Period, 14:24, Bruins 1-0: The Bruins will be shorthanded again, as Zdeno Chara now heads to the box for tripping as the Flyers have taking over the momentum in the last few minutes.
First Period, 13:58, Bruins 1-0: The Bruins do no better with their power-play chance, as the Flyers nearly score on a shorthanded 2 on 1, but Thomas flashed the glove to stop Eric Wellwood's bid from the left wing.
Thomas then came up big as he stopped Jagr in alone on a clean breakaway out of the box.
First Period, 11:58, Bruins 1-0: The Flyers don't muster much on that power play. Patrice Bergeron had the best scoring chance with a shorthanded bid and a follow-up at the right post, then Jaromir Jagr negated the rest of the man advantage with a tripping penalty. It will be 4 on 4 for 39 seconds before the Bruins go on the power play.
First Period, 10:37, Bruins 1-0: The Flyers finally put some pressure on the Bruins, testing Thomas with three shots and now will go on the power play as Jordan Caron heads to the box for hooking.
First Period, 6:23, Bruins 1-0: The Bruins finally strike first in a game, as Chris Kelly bangs home a rebound in front.
Benoit Pouliot had the initial shot from the left wing and Kelly followed up by driving the net and chipping in the rebound from the low slot. The Bruins are up 5-0 in shots as they finally get off to a strong start in a game.
First Period, 5:07, 0-0: Flyers defenseman Andreas Lilja goes off in pain, heading to locker room after taking a shot up high in front of the net.
First Period, 3:12, 0-0: The nastiness continues with Adam McQuaid delivering a hit on Scott Hartnell, then challenging him. Hartnell wants no part, but does exchange slashes with Chara after they bump. No penalties are called on the play.
First Period, 1:55, 0-0: The gloves are shed less than two minutes into this one, with Gregory Campbell squaring off with Zac Rinaldo.
It was a long scrap with some wild swings, though not a lot was landed by either player. Each gets five for fighting and we'll stay at even strength.
First Period, 0:00, 0-0: The Bruins are back in their customary black and gold after taking the warm-ups in special green jerseys for St. Patrick's Day, and this key game for the Bruins is under way here at the Garden.
1 p.m.: The Bruins will open with Milan Lucic, David Krejci and Jordan Caron up front, Zdeno Chara and Dennis Seidenberg on defense and Tim Thomas in goal.
The Flyers counter with their top line of Scott Hartnell, Claude Giroux and Jaromir Jagr, with Matt Carle and Kimmo Timonen on the blue line and Ilya Bryzgalov in net.
12:55 p.m.: The Bruins have officially scratched Joe Corvo, Mike Mottau and Trent Whitfield.
Andrej Meszaros, Pavel Kubina and Jody Shelley are out for the Flyers.
12:45 p.m.: The Bruins reunited Zdeno Chara and Dennis Seidenberg as a pairing in the warm-ups, and could go with that to try to snap out of their current slump.
Greg Zanon was with Adam McQuaid in the line rushes. Mike Mottau was on the ice, but not in the line rushes, so it appears Mottau will join Joe Corvo as the healthy scratches on defense.
The full line combinations from the warm-up:
12:30 p.m.: Tim Thomas and Ilya Bryzgalov lead the teams out for warm-ups. That will be the goaltending matchup in this one.
Bryzgalov is 7-0-0 with a 0.99 GAA, .965 save percentage and four shutouts in his last seven starts.
12 p.m.: The Bruins will try to snap a four-game losing streak and retake first in the Northeast Division when they take on the Flyers in about an hour.
They'll do it without Joe Corvo. the struggling defenseman will be a healthy scratch. The other scratch on defense will be decided after the warm-ups.
8 a.m. ET: The Bruins return home looking to snap a season-high four-game losing streak when they host Philadelphia in a St. Patrick's Day matinee at the Garden.
They'll have to do it against a Flyers team that comes in 7-1-0 in March. And they'll have to do it while not leading the Northeast Division for the first time since Nov. 30.
Ottawa passed Boston with a 2-1 overtime win over Montreal on Friday. The Bruins still have two games in hand on the Senators, but they have to finally start taking advantage of those extra games.
That won't be easy against Philadelphia (41-22-7, 89 points), which suddenly has found an answer to its long-standing issues in goal with Ilya Bryzgalov going 7-0-0 with an 0.99 GAA, .965 save percentage and four shutouts in March. That included a shutout streak of 249:43 that was snapped by the Islanders on Thursday, though the Flyers still held on for a 3-2 win.
The Bruins (40-27-3, 83 points) lost to Philadelphia 2-1 after raising their Stanley Cup banner in the season opener on Oct. 6, but beat the Flyers 6-0 and 6-5 in a shootout in Philadelphia on Dec. 17 and Jan. 22. That most recent game was the last played by Nathan Horton, who suffered a concussion on a controversial hit from Flyers forward Tom Sestito. Horton remains out, but the Bruins won't get a chance to address any issues directly with Sestito, who is out himself with a torn groin.
The puck drops at 1 p.m. Tune in to NESN to watch the game, and stay with the NESN.com live blog, as we'll keep you up to speed on everything happening at the Garden.