Overbay drove in two runs, and Edwin Encarnacion and Joe Inglett also drove in runs for the Blue Jays, who played an inspired game about 30 minutes after learning that teammate Alex Rios had been claimed off waivers by the Chicago White Sox.
Shawn Camp (1-5) picked up the win in relief of ineffective starter Marc Rzepczynski, who allowed three homers and didn't make it out of the fourth. The Blue Jays bullpen allowed four hits over 5 2/3 shutout innings, helping Toronto win for just the third time in 10 tries against the Yankees this season.
Jason Frasor worked around a single in the ninth by Hideki Matsui for his fifth save.
On one of the hottest days to blister New York this summer, the sizzling Yankees came in fresh off a four-game sweep of bitter rival Boston. They'd also built their biggest lead in the division (6 1/2 games) since winning the AL East by 10 games in 2006.
For a while, it looked like the roll would continue.
Derek Jeter hit a leadoff homer on the third pitch he saw, and Robinson Cano and Jerry Hairston added back-to-back homers in the fourth. But the bats finally went quiet against the Blue Jays' vastly underrated bullpen, and Toronto pushed its modest winning streak to three straight for the first time since June 21-24.
Yankees starter Sergio Mitre (1-1), who could be fighting for his spot in the rotation, allowed five runs — three earned — on six hits over five innings.
He got into trouble in the third, when Hill homered off the top of the wall in left field for the first run allowed by a New York starter in more than 24 innings.
Before the Blue Jays took the field again, plate umpire Paul Schrieber quietly ejected Toronto manager Cito Gaston — keeping him from watching the fireworks in person.
The Yankees regained the lead on a sacrifice fly by Nick Swisher before the Blue Jays scored three times in the fourth inning. Overbay walked and Vernon Wells singled before Jose Bautista hit a hot shot at Mitre, who made a nice backhanded snare and wide throw to second. Cano couldn't gather it in, the ball trickled into center and Overbay scored easily.
Encarnacion added a sacrifice fly, and Inglett hit an RBI triple down the right-field line.
The homers by Cano and Hairston were the 12th back-to-back for the Yankees this season, and the second in as many games, after Johnny Damon and Mark Teixeira did it in the eighth inning of a 5-2 victory over the Red Sox on Sunday night.
Overbay's go-ahead homer in the fifth came on a 3-2 count with two outs and soared over the Yankees bullpen before bouncing just below the first row of seats in deep right field.
Rzepczynski, who was charged with the loss against the Yankees last week, allowed four runs on seven hits in 3 1/3 innings. Even though he was long gone, the Blue Jays managed to win for only the second time in the seven games he's started.
NOTES: The Blue Jays did not get a player for Rios. Rather, the White Sox assume his entire contract. … Yankees infielder Cody Ransom, who was designated for assignment, signed a minor league contract and will go to Triple-A Scranton/Wilkes-Barre. … Yankees OF Brett Gardner (broken left thumb) showed up at the ballpark without a cast on his hand.