Halladay (15-9) improved to 13-5 in 30 career games against the Yankees, allowing three runs and five hits in seven innings. He walked two and matched a season high with nine strikeouts.
Pitching for the first time since spraining an ankle at Detroit last Wednesday, Scott Downs worked the eighth before Brandon League wrapped it up in the ninth.
Joe Inglett had a career-high four hits, Scutaro matched career highs with four hits and four RBIs as Toronto had 21 hits in all, one shy of a club high this season.
Alex Rios, Adam Lind each had three hits for the Blue Jays, and Rios and Matt Stairs drove in three runs each.
Sidney Ponson (7-4) matched a season high by allowing seven runs and eight hits in two-plus innings. He walked one and didn't strike out a batter. The right-hander has won twice in 10 starts since New York signed him June 19.
Right-hander David Robertson allowed two runs in 1 1-3 innings and left-hander Billy Traber was tagged for four runs and seven hits in 2 1-3 as the Yankee bullpen absorbed a beating.
Rios singled home a run in the first and Rod Barajas' second-inning sacrifice fly made it 2-0 before Toronto broke it open with a five-run third, sending 10 men to the plate.
Inglett and Scutaro began the inning with back-to-back singles and scored on Rios' double before Vernon Wells walked. Lind chased Ponson with an RBI single. After walking Lyle Overbay, Robertson got two outs, then gave up a two-run, broken-bat single to John McDonald.
The Blue Jays added three more in the fourth on a bases-loaded double by Stairs before Scutaro drilled a three-run drive to left in the fifth, his fifth.
Toronto finally came up empty in the sixth, when Edwar Ramirez came on to strike out Scutaro, leaving the bases loaded.
Blanked by Halladay through the first six innings, New York got on the board in the seventh when Hideki Matsui hit a three-run homer to right, his eighth. Matsui, who returned Tuesday after missing 49 games due to a sore left knee, homered for the first time since June 12 at Oakland.
Wells, who finished 0-for-4 with a walk, was the only Toronto starter not to get a hit.
