Halladay pitched his major league-leading ninth complete game to become the American League's second 20-game winner and the Blue Jays beat the New York Yankees 8-2 on Thursday night.
Vernon Wells homered and drove in four runs as Toronto snapped the Yankees' seven-game winning streak.
Halladay (20-11) improved to 5-1 in six starts against the Yankees this season and posted his second career 20-win season. The right-hander went 22-7 with nine complete games in 2003, when he won the AL Cy Young award.
Halladay, who joined Cleveland's Cliff Lee as a 20-game winner, gave up two runs and six hits. He walked one and struck out five, giving him 206 for the season, a career-high.
"All you've got to do is take a look at his numbers and know that he's probably the best starter in baseball," said New York outfielder Brett Gardner, who went 3-for-4. "Without a doubt he's one of the best, if not the best, starter in the league."
Halladay's gem came hours after the Blue Jays announced that manager Cito Gaston had signed a two-year contract extension, and that general manager J.P. Ricciardi would return in 2009. Toronto has not reached the postseason under Ricciardi, who was hired before the 2002 season.
Halladay is pleased that Gaston and Ricciardi will be back next spring.
"I like what Cito has done in the time he's been here," Halladay said. "I think we've gone in some good directions and I've always trusted J.P. There's probably been times when as players we've underachieved and I think that reflects poorly on him, but that wasn't necessarily his decision-making. I like that they're coming back. I feel confident the organization will continue to go the right way."
Wells hit a two-run homer in the third and added a two-run single in the fourth as the Blue Jays closed out the home portion of their schedule with a 47-34 record.
Carl Pavano (4-2) allowed five runs and eight hits in 3 2/3 innings, his shortest outing since coming off the disabled list last month.
"I got myself into a quite a few jams I couldn't get out of," Pavano said. "It's a game of making pitches when you need to and I didn't. I was up, the ball was up. These last couple of starts, the ball has been flat and I've been getting myself into jams, getting out of jams."
It was likely the final start in a Yankees uniform for Pavano, whose four-year, $40-million contract expires after the season. The oft-injured right-hander went 9-8 in 26 starts for New York.
"It's been crazy," Pavano said of his time with the Yankees. "It seems like I've just been fighting an uphill battle. That's part of the adversity that comes with this game, that's part of life. Nothing is ever going to run smoothly. I think I dealt with it the best I could, I made adjustments where I needed to. What are you going to do? You just keep moving forward."
Of greater concern to the Yankees was the health of closer Mariano Rivera, who returned to New York on Thursday for an MRI on his shoulder. He'll rejoin the team Friday in Boston, and manager Joe Girardi said he expects Rivera to be available.
Before the game, Girardi said Rivera had told him that "his whole body was a little cranky," but general manager Brian Cashman told reporters that Rivera had complained of a sore shoulder.
The Yankees opened the scoring in the third when Gardner doubled and scored on Robinson Cano's single.
Wells put Toronto ahead with his 18th homer in the bottom half, and the Blue Jays chased Pavano with a three-run fourth.
New York got one back in the fifth, with Cody Ransom scoring when Francisco Cervelli grounded into a double play, but the Blue Jays added two in the bottom half against reliever Dan Giese. Scott Rolen singled before consecutive doubles by Travis Snider and Gregg Zaun made it 7-2.
Scutaro made it 8-2 with an RBI single in the seventh against Humberto Sanchez.
The Yankees held Johnny Damon, Derek Jeter and Alex Rodriguez out of the lineup, with Ransom, Wilson Betemit and Melky Cabrera starting instead. Cervelli made his major league debut behind the plate. Girardi said he will put his regulars back in the lineup at Boston on Friday.
New York and Toronto split the season series 9-9. ... The crowd of 44,346 pushed Toronto's total attendance to 2,399,786.