Boston is off Monday before opening a three-game series Tuesday night in the Bronx.
"Any series we have with New York is going to be a big series, but when we come off of a win like this, I feel like everyone will show up and just have a little more energy and be able to feed off this game," Lowrie said.
Coco Crisp also homered for Boston, which has won 11 of 16 on the road. Jonathan Papelbon (5-3) worked two scoreless innings and Manny Delcarmen closed it out for his second career save and first this season.
Manager Terry Francona called it "one of the funnest games I've been a part of in a long time."
"It was a great win," Francona said. "We've got a day to regroup and we probably need to."
Left fielder Jason Bay, who made a leaping catch at the wall in extra innings, called it a "huge win" for Boston, which leads the AL wild-card race.
"A few of us were talking that it's probably a lot bigger than just a regular win, given the way [the Blue Jays] are playing and that they're trying to catch up to us," Bay said.
Lowrie hit a one-out drive to right, his second big league homer, off right-hander Brandon League (0-2), who had not allowed a run in his previous 12 appearances. Lowrie, playing third base, also threw out a runner at the plate on a sixth-inning relay.
"He continues to impact the game and we'll take it. We need it," Francona said. "He's stepped in and been a valuable member of our ballclub."
Vernon Wells put Toronto in front with a two-run homer in the first, his third homer in two games and team-leading 13th.
"The minute you make a mistake, Vernon Wells hits it 400 feet," Francona said.
Boston moved in front with a four-run fourth. Alex Cora and Crisp drew one-out walks and, after Jacoby Ellsbury popped out, Pedroia hit his 14th homer. David Ortiz followed with a double and scored on Kevin Youkilis' single.
Adam Lind hit a line drive to deep right in the bottom half that Ellsbury caught before crashing at full speed into the chain-link fence in front of the bullpen.
"I knew I was closing in on the fence," Ellsbury said. "I hit the wall pretty good."
A dazed Ellsbury stayed down for several minutes and was checked by trainer Paul Lessard, but remained in the game.
Lowrie said Ellsbury, who had several cuts and grazes around his eye and on his shoulder, "looked like he just got done with a 15-round fight."
Francona saluted Ellsbury for staying in, knowing that J.D. Drew (sore back) was unavailable for the sixth straight game.
"The fact that [Ellsbury] stayed in and played that game, it might be a little over-dramatic, but I thought he grew up a little bit today," Francona said. "He understood where we were physically with the rest of our team and what he can do by staying in the game. I thought that was huge."
Ellsbury couldn't help when the next batter, Lyle Overbay, put one over the right-field wall for a solo homer, his 11th, cutting it to 4-3.
The Blue Jays took a 5-4 lead with two in the sixth. Alex Rios led off with a single and scored on Wells' double to left-center. Wells moved to third on Lind's grounder, Overbay struck out and Matt Stairs was intentionally walked to bring up Rod Barajas, who hit an RBI double down the third-base line. Stairs tried to score from first but was thrown out at the plate on Lowrie's relay.
Toronto's lead was short-lived. Crisp led off the seventh with a homer to right, his seventh, making it 5-all.
Rios hit a deep drive to left off Papelbon in the 10th, but Bay ended the inning with an acrobatic catch.
"I got up on the wall there and got up as high as I could and made the catch," Bay said. "It was a big time for it, too."
Boston starter Daisuke Matsuzaka allowed five runs and eight hits in six innings. He walked one and struck out eight.
The Japanese right-hander had allowed just five earned runs in four previous starts this month, all wins, and had won six of his past seven outings.
Matsuzaka gave up two homers in a game for just the second time this season. The last time he allowed a home run away from Fenway Park was April 1 at Oakland, when Jack Cust hit a solo shot in Boston's 2-1 win.
Toronto right-hander A.J. Burnett, who had won six straight starts and 10 of 12, allowed five runs and seven hits in seven innings. He walked three and struck out seven.
RHP David Pauley joined the Red Sox before the game. Pauley was called up from Triple-A Pawtucket when RHP David Aardsma (groin) was placed on the 15-day DL. ... The Blue Jays said RHP Jesse Litsch (9-7), who has thrown 13 scoreless innings over two starts since being promoted from Triple-A on Aug. 12, will pitch Thursday at Tampa Bay instead of LHP John Parrish.