In the opener, Robinson Cano and Chris Stewart each hit three-run homers to rally the Yankees from four runs down to beat the Blue Jays 8-4. Toronto lost slugger Jose Bautista to a sore hip early in the game.
Cano had an RBI single in the second game and had six hits and five RBIs for New York in the two games.
Ichiro Suzuki singled and doubled in the first game, leaving him one shy of 4,000 combined hits during his careers in Japan and the major leagues.
With fans standing and chanting "Ichi-ro!" in the eighth, he grounded out. Suzuki pinch ran in the second game and scored the winning run.
With a full moon hanging over the right field rafters, Darren Oliver (3-4) walked Mark Reynolds to start the ninth.
Suzuki pinch ran and advanced on Eduardo Nunez's sacrifice bunt. Suzuki stole third before scoring on Nix's line drive to left that gave the Yankees their eighth win in 11 games.
Mariano Rivera (4-2) worked out of a two-on jam in the top of the ninth for the win. Anthony Gose failed to get down a sacrifice bunt in the top of the ninth.
The Blue Jays extended their record with an 11th straight loss in New York.
Mark Buehrle was on track to end an eight-decision losing streak to New York but he gave up a tying homer in the seventh to Nix, the infielder's first homer since June 25th.
Nix was the Yankees' second unlikely long ball hitter of the day. Stewart connected off Neil Wagner (2-4) in the sixth inning for his first homer since May 15 — that's 173 homerless at-bats — to put New York ahead in the opener.
Just 1-10 in his career against the Yankees, the left-hander shut down a rejuvenated lineup by allowing two runs and six hits in 6 2-3 innings. He struck out Alex Rodriguez all three times he faced him.
Rajai Davis had a two-run double in the first game, and was responsible for the Blue Jays' first two runs in Game 2. He scored on Phil Hughes' wild pitch in the first inning and had a sacrifice fly in the fifth inning to put Toronto up 2-1.
In the opener, Cano got his 200th career home run off Esmil Rogers in the third and had four hits. His drive in the third pulled New York to 4-3 after Toronto went up 4-0 in the second against Ivan Nova (7-4). Cano added an RBI double in the seventh.
Bautista was removed from the team's seventh straight loss to the Yankees before the bottom of the fourth inning because of soreness in his left hip. The Blue Jays last lost seven in a row to New York in 1999.
Manager John Gibbons said Bautista was having tests on the hip and he might be out at least couple of games.
Maicer Izturis left the nightcap after grounding out to end the fifth inning because of a sprained left ankle.
During the afternoon game, Major League Baseball announced Yankees manager Joe Girardi was fined $5,000 for his on-field tirade after Boston's Ryan Dempster hit Rodriguez with a pitch on Sunday. Dempster was suspended five games and fined $2,500.
Girardi refused to comment on the suspension and fines but did reiterate what he said earlier in the day, that he's worried a light penalty would encourage "open season" on Rodriguez.
"We'll find out," Girardi said. "I sure hope not."
Rodriguez singled to start the sixth — to cheers — and he scored on Stewart's fourth homer of the season, a shot to left field off Wagner that put New York ahead 6-4.
But Rodriguez struck out five times in the doubleheader in seven at-bats. He came up with two on in the eighth inning of late game, but grounded into a double play.
Nova allowed four runs in the second inning when Toronto batted around in the makeup of a rained-out game on May 19.
Kevin Pillar got his first big league hit in the night game — in his 18th at-bat, a liner over a leaping Cano.
Cano tossed the ball to the Blue Jays dugout and Jose Reyes pretended to throw it into the crowd. Pillar stood on first smiling broadly. The 24-year-old from California went 0 for 4 in the opener but got his first RBI.