The Red Sox rallied from a 3-0 deficit to snap a four-game skid and head into their final series with a one-game lead over Tampa Bay.
Boston held a nine-game lead over the Rays entering play Sept. 4 but has gone 5-16 since then. Up by 1 1/2 games to start the day, the Red Sox nearly wasted that entire lead after losing the opener 6-2 despite Ellsbury's two homers. Combined with the Rays' 5-2 win over Toronto, the Red Sox went into the second game with a half-game lead.
Boston finishes in Baltimore, while Tampa Bay hosts the Yankees, who already have clinched the AL's best record and homefield advantage through the AL championship series.
"I hope we were breathing before — every other breath. It was a big win, but we've got to go down tomorrow and play well," Red Sox manager Terry Francona said.
Ellsbury homered off Scott Proctor (0-2) after Darnell McDonald singled and Marco Scutaro walked.
Franklin Morales (1-1) pitched two innings for the win. Felix Doubront, recalled on Sept. 1, finished the five-hour, 11-minute game for his first save since August 2010.
In the opener, A.J. Burnett made his most impressive start in nearly three months and Jorge Posada hit a two-run homer for the Yankees. Ellsbury connected twice to become the first player in Red Sox history to reach 30 homers and 30 stolen bases in a season.
Desperate for a win in the second game, Terry Francona used Jonathan Papelbon for a season-high 2 1/3 innings, bringing the closer in with the score tied on the road.
Typical of the bumbling baseball they've played while going 6-18 in September, the Red Sox made three more errors Sunday, several miscues on the basepaths and blew an opportunity to advance the runner in the 10th inning with a sacrifice. They had the leadoff runner reach in each inning from the sixth through the 10th in the nightcap.
Yet they still won.
Yankees manager Joe Girardi was ejected for the third time this season when he raced onto the field in the 13th to protect first baseman Nick Swisher and dispute a call after Tim McClelland called Dustin Perdroia safe. Replays show the diving Pedroia was out.
The Red Sox fell behind in the first inning for the third straight game in New York, but rallied to take a 4-3 lead in the seventh.
The Yankees tied it, though, in the bottom half on a sacrifice fly by Chris Dickerson, the only New York player to start both games.
The Red Sox fell behind in the first, making their third error of the doubleheader and 17th in 12 games.
With two on against John Lackey, Mark Teixeira hit a drive off the top of the fence in right-center. Teixeira went for third on the throw home and was able to score when catcher Jason Varitek threw the ball into left field.
The offense, meanwhile, woke up in the fifth after going 6-for-30 in the opener. Jed Lowrie hit a drive that hit off the wall in right field under the glove of a leaping Swisher for a triple. J.D. Drew, playing for the first time since July 19 because of a shoulder injury, singled him home for the first run off Ivan Nova in 15 innings.
Adrian Gonzalez's RBI single and Scutaro's run-scoring double tied it in the sixth, and Varitek singled for a 4-3 lead in the seventh.
In the opener, the Yankees raced to a 2-0 lead behind two bunt singles and some poor play by the Red Sox. Catcher Jarrod Saltalamacchia had an error and a passed ball. Carl Crawford made an error in left field that led to a run in the fifth.
Tim Wakefield (7-8) pitched four-plus innings, giving up five runs — three earned — five hits and five walks.
Batting fourth for the first time since 2009, Jorge Posada connected in the third inning for his fifth homer against the knuckleballer. The 40-year-old with a diminished role this year was given a curtain call.
Burnett (11-11) allowed five hits — three to Ellsbury — and two runs in 7 2/3 innings — his first outing of more than six innings since he went eight on July 29.
Derek Jeter had three hits to lift his average to .300 at the end of the game for the first time since April 2. Starting with July 9, the day he reached 3,000 hits, he is batting .346 following a .257 start.
Notes:
Robinson Cano grounded out against Daniel Bard in the eighth and is 0-for-8 lifetime against the reliever. … Red Sox RHP Clay Buchholz, who hasn't pitched since June 16 because of a stress fracture in his lower back, will pitch an inning for Boston's instructional league at Fort Myers, Fla., on Monday. If all goes well, he could pitch an inning or two Wednesday at Baltimore. … Red Sox reliever Scott Atchison tweaked his right groin while warming up for the eighth inning of the first game and had to leave. … There were 209 homers at Yankee Stadium this year, down from 223 during the 2010 regular season and a major league-leading 237 in its opening year in 2009. There were nine games with no homers, up from seven last year and just one in 2009. … The Yankees averaged 45,107 in attendance this year after drawing 98,613 for the doubleheader. New York led the majors last year at 46,491 and averaged 45,918 in the stadium's opening season. The Yankees had 20 sellouts, up from 15 last year and seven in 2009.