Leiter (2-3) gave up four hits in 5 2/3 scoreless innings, walking four and striking out two in his fifth start with New York.
Before the game, the Yankees found out that Randy Johnson's next start is in doubt because of a bad back and that Carl Pavano will see Dr. James Andrews in Alabama on Monday instead of making a minor-league rehab start.
"That makes it even more necessary to count on Al," manager Joe Torre said. "Leiter was huge for us today. We need to count on guys who have been down that road before and he's one of them."
Leiter beat Boston in his debut on July 17 but lost his next three starts.
"I know why I'm here," Leiter said. "I think it's only going to get better for me. I feel much more comfortable about what I'm doing here."
Leiter was 3-7 with a 6.64 ERA in 17 games for the Marlins, who designated him for assignment last month. Before the game, Torre said there was no way Leiter could have lost his ability to pitch so quickly. He went 10-8 with 3.21 ERA last year for the Mets.
The left-hander came up with New York in 1987 and was traded to Toronto in 1989.
Leiter took a three-hit shutout into the sixth but was replaced by Alan Embree after walking Frank Menechino to load the bases. Embree escaped the jam as Orlando Hudson popped up on Embree's first pitch.
"Believe it or not, you get some of those veteran pitchers and they can get in some jams and come up with a pitch here or there," Toronto manager John Gibbons said.
Mariano Rivera got the final out with runners on first and second to earn his 29th straight save.
Pinch-hitter Eric Hinske drove in the first run for the Blue Jays with a sacrifice fly in the eighth. Left-fielder Hideki Matsui
thought Hinske's fly ball was the third out of the inning and was about to throw the ball to a fan in the stands before realizing it was the just the second out. He then threw out Gregg Zaun at third for the third out, prompting some smiles from his teammates.
Matsui realized it was only the second out after looking at the fans and hearing his teammates scream.
"Usually when there is three outs the fans in the stands are looking to get the ball, so when I was about to toss the ball they didn't seem like they wanted it," Matsui said through an interpreter. "There was no doubt I was pretty embarrassed. Even a little-leaguer wouldn't make that kind of mental mistake."
Rodriguez couldn't believe it.
"I've never seen Matsui ever make a mistake. That's the weirdest thing," Rodriguez said.
Towers allowed five runs -- three earned -- and 10 hits in six innings.
"He was in trouble but he hung in there," Gibbons said.
Giambi's RBI single off Jason Frasor gave New York a 6-0 lead in the seventh.
New York center fielder Bernie Williams didn't play because of sore right shoulder. Williams jammed it while making a catch in the ninth inning of Saturday's game. Torre said he's day-to-day. ... First baseman Martinez robbed Zaun of a hit with a diving catch in the second. Toronto second baseman Hudson robbed Matsui of a hit with a diving stop of a grounder in the third. ... Toronto ace Roy Halladay threw on the side on Sunday. General manager J.P. Ricciardi said he'll return within a week to 10 days. The 2003 AL Cy Young Award winner was struck in the left shin by a line drive off the bat of Texas' Kevin Mench on July 8.