Carlson (7-2) had not allowed a run in 14 innings.
Jose Veras (5-2) worked one inning for the win.
Making just his second start since April 29 after missing much of the season with a stress fracture in his rib, New York right-hander Phil Hughes pitched eight innings but failed to post his first win of the season. He allowed two runs and five hits, walked none and struck out a season-high six.
Toronto scored in the first when Joe Inglett led off with a double, went to third on Marco Scutaro's grounder and scored on Alex Rios' sacrifice fly.
The Yankees scored twice in the third, thanks in part to Scutaro's throwing error. With Gardner at first on a fielder's choice, Cano lined a single off Toronto starter A.J. Burnett's thigh. The ball rolled to Scutaro at shortstop and his throw to first sailed wide, moving up both runners. Xavier Nady drove in both with a two-out single to center.
Hughes had retired 18 of 20 before Toronto tied it in the seventh when Scott Rolen hit a two-out solo homer to left, his 11th.
Burnett allowed two runs - one earned - and seven hits in eight innings. He walked two and struck out 11.
The right-hander can opt out of the final two years of his contract after the season, meaning this could have been his final start with Toronto. The crowd of 28,701 gave Burnett a standing ovation when manager Cito Gaston replaced him before the ninth, then called him out of the dugout for a curtain call.
Yankees shortstop Derek Jeter, who was hit by a pitch Saturday, missed his second straight start because of a sore left hand. Jeter did not take part in batting practice but could play Thursday, manager Joe Girardi said.
With New York eliminated from the postseason, regulars Johnny Damon and Alex Rodriguez were also held out of the starting lineup, although Damon came on as a pinch-runner in the ninth. Cody Ransom made his second straight start at shortstop, with Wilson Betemit taking over at third, Miranda playing first and Moeller starting at catcher.
Notes: New York LHP Andy Pettitte will not make his final start of the season, Saturday at Boston, because of a sore shoulder. RHP Sidney Ponson will start. ... Toronto 2B Aaron Hill, out since May 29 because of a concussion, rejoined the team Wednesday and will visit a neurologist Thursday. Hill said he is symptom-free following three weeks of inactivity. ... Toronto Maple Leafs goalie Curtis Joseph attended the game.
