TORONTO -- For the first time in more than four months, Chris Capuano went home with a W next to his name.
Capuano (2-3) pitched 6 1/3 innings in his first win in seven starts since joining the Yankees. The veteran left-hander, who was acquired last month in a trade with Colorado, allowed three runs, two earned, and eight hits.
"I couldn't be prouder to get a win as a Yankee," Capuano said. "It feels really good."
David Robertson got the final four outs for his 35th save in 38 chances.
"We've just got swing our way out of it," manager John Gibbons said. "We're better hitters than what we're producing as a whole right now."
Mark Buehrle (11-9) allowed four runs and seven hits in six-plus innings in another loss to New York.
Bautista put the Blue Jays in front with a second-deck homer in the fourth, his third in three games. It's the first time Bautista has connected in three straight games since July 1-3, 2011.
New York answered with a five-run seventh, with the first four batters reaching against Buehrle. Brian McCann doubled, Carlos Beltran walked and Brett Gardner hit an RBI double, with Beltran scoring on an errant relay throw by second baseman Steve Tolleson.
Aaron Loup came on after Ichiro Suzuki's infield single, and Gardner made it 3-1 when he scored on a wild pickoff throw by catcher Navarro. Two pitches later, Ellsbury lined a two-run homer to right. It was the first homer by a left-handed batter in Loup's career, snapping a streak of 233 at-bats.
Buehrle dropped to 1-13 with a 6.14 ERA in 20 career starts against New York. The lefty is 0-11 in his last 16 outings against the Yankees.
"It's not like we're all running to the bat racks because Buehrle is pitching," New York's Derek Jeter said. "I think that's just a fluke thing."
More importantly for the sliding Blue Jays, Buehrle is 1-8 in his last 15 starts this season.
Headley made it 6-3 with a first-pitch homer off Dustin McGowan in the ninth. Ellsbury followed with a triple but was out at the plate trying to score on Jeter's grounder to third, injuring his left ankle as he slid into Navarro.
Ellsbury stayed in the game and X-rays were negative, but manager Joe Girardi said his status for Saturday was in doubt.
"It's frustrating because he's playing so well," Girardi said.
Jeter got a standing ovation from the crowd of 43,318 before the first at bat of his final scheduled series in Toronto. He'll be honored with a gift and ceremony before Sunday's finale. Asked before the game for a defining memory of his career in Canada, Jeter referenced opening day in 2003 when he injured his shoulder in a collision with Blue Jays C Ken Huckaby. "The first thing I think about is dislocating my shoulder," Jeter said. "I don't know if that's a good thing."
Capuano said going up against Buehrle, one of the fastest-working pitchers in baseball, presented him with a unique problem. "I didn't even have time to use the bathroom, if I needed to, between innings," said Capuano, who finally found relief during New York's five-run seventh.
Yankees: Injured Yankees ace Masahiro Tanaka is being sent back to New York because of general soreness in his right arm. Tanaka will play light catch and work out every day at Yankee Stadium over the weekend, but Girardi said it would be "maybe a week" before Tanaka throws another bullpen.
Blue Jays: OF Colby Rasmus returned to the lineup at DH after missing the previous two games with an illness. ... RHP Brandon Morrow (right index finger) will make his second rehab appearance on Saturday, this time with Triple-A Buffalo. Morrow threw one scoreless inning for Class-A Dunedin on Wednesday.
Yankees RHP Michael Pineda (3-2) faces Blue Jays RHP Drew Hutchison (8-11) on Saturday. Pineda is 1-0 with a 2.08 ERA in three starts since returning from the disabled list after missing 87 games with a sore shoulder.