Gagne played for the first time since he broke his right toe in Game 4 of Philadelphia's opening-round series against New Jersey.
Game 5 is Monday at Boston. The Bruins can still advance to their first conference finals since 1992 with a win on their home ice.
Former Flyers star Mark Recchi scored twice for the Bruins — including the tying goal with 31.5 seconds left in regulation that made it 4-all.
Chris Pronger, Danny Briere, Claude Giroux and Ville Leino all scored for the Flyers.
Michael Ryder and Milan Lucic had Boston's other goals.
Gagne was expected to at least miss this round after being injured while blocking a shot. He was walking around the Flyers' practice facility this week and was hopeful he could start skating this weekend.
He managed an early comeback and heard a rousing ovation when he was introduced in pregame introductions. Gagne got the crowd roaring 3 1/2 hours later on his first goal of the postseason.
The Flyers wasted a 3-1 lead and were deflated when Recchi scored the tying goal.
Recchi burned his former team when he scored against Brian Boucher off a faceoff in Philadelphia's end. The sounds of "Booooosh" that echoed after every late save turned to "booooo" after the Flyers were headed to OT. It was Recchi's sixth goal of the postseason.
The Flyers appeared to have forced Game 5 minutes earlier in the third. Leino skated across the slot and tipped in Pronger's shot with 5:40 left for a 4-3 lead that sent the crowd into a frenzy.