Pettitte pitched six effective innings, and Curtis Granderson homered to help the surging Yankees win 5-3 on Thursday after a 3 1/2-hour rain delay, their 10th straight victory over the Blue Jays.
New York took advantage of a missed call by the umpires to win its fifth consecutive game and 10th in 12 overall.
"We're feeling good about ourselves, and you knew this was going to happen," Pettitte said. "It was just a matter of when, and you hope it's not too late."
Eduardo Nunez hit a two-run single for the Yankees, who improved to 12-1 against Toronto this season with their second four-game sweep of the Blue Jays. New York moved within 3 1/2 games of the second AL wild-card spot heading into a weekend series at Tampa Bay.
"We've got a good shot," Granderson said. "We still control our destiny."
The Yankees have won 13 home games in a row against Toronto, their longest streak against one team since a 14-game run vs. Kansas City from August 2002 to April 2006.
The last-place Blue Jays have lost five straight and 11 of 15. The only other opponent to sweep a pair of four-game series from them in one season was the 1978 Milwaukee Brewers.
Toronto had a lead in every game of this series, just as it did during New York's four-game whitewash at Yankee Stadium in late April. The Blue Jays have dropped 22 of 24 in the Bronx, dating to 2011. Their 10-game skid vs. New York is their longest against one team in a single season since losing 11 in a row against Boston in 2002.
"It's hard. Yankee Stadium is a tough place. The sad part is we're in every game, basically all year. We just couldn't put them away with a lead," said manager John Gibbons, ejected in the fifth.
Rodriguez made a pair of important defensive plays at third base and worked a walk that started a rally.
Pettitte (9-9) gave up four hits and three walks to win his second consecutive start after going 0-3 in his previous five. His only blemish was J.P. Arencibia's leadoff homer in the fifth.
With his 254th victory, the 41-year-old lefty tied Jack Morris and Hall of Famer Red Faber for 42nd place on the career list.
After the Blue Jays scored twice off Shawn Kelley in the seventh, Boone Logan struck out pinch-hitter Adam Lind with two on to preserve a 5-3 lead.
Preston Claiborne, just recalled from the minors, worked a scoreless eighth, and David Robertson pitched a perfect ninth for his second save. Mariano Rivera was rested after appearing in three games over the previous two days.
"Each day you're able to make up a little ground, it seems more attainable — and that's good for the guys in that room," Yankees manager Joe Girardi said.
The start was delayed for 3 hours, 32 minutes — though it wasn't raining when play was supposed to begin. Light, steady showers fell throughout much of the delay, and the game didn't start until the storm front cleared.
The sun broke through as Pettitte trotted out to the mound to begin his warmups.
Aided by an incorrect call, the Yankees took a 2-1 lead against J.A. Happ (3-3) on a confusing play in the fifth.
With the bases loaded and one out, Vernon Wells hit a sinking liner to centre that was caught by a tumbling Rajai Davis just before it hit the ground. But the umpires ruled it a trap as Nunez scored the go-ahead run.
Thinking the ball had been caught, Chris Stewart tried to scramble back to second and was thrown out by Davis — after he fumbled the transfer. Gibbons came out to argue the ball was caught. Instead, Wells was credited with an RBI on an 8-4 fielder's choice.
"We scored a run, that's all that matters," he said.
Gibbons was ejected, for the fifth time this season, by first base ump Scott Barry. Toronto pitcher Mark Buehrle was tossed by third base umpire Ted Barrett for yelling from the bench.
"We looked at the replay and it looked to us like it bounced, but probably inside his glove," said Barrett, the crew chief. "So on replay, probably would have been ruled a catch."
One inning later, Rodriguez drew the first of three straight Yankees walks before Nunez delivered a two-run single. Toronto third baseman Brett Lawrie made an outstanding play on Stewart's RBI groundout that made it 5-1.
Rodriguez charged in to throw out Lawrie on a slow bouncer in the fourth, saving a run. The third baseman, who returned this month from hip surgery and a strained quadriceps, also grabbed a sharp grounder and stepped on the bag to start an inning-ending double play with the bases loaded in the fifth.
"Just smoked, right down the line. I mean, I just put my glove down. That ball caught me, almost," he said. "That was a big play."
Granderson led off the bottom half and homered into the second deck in right, tying it at 1.
NOTES: Yankees CF Brett Gardner was rested. He entered for defence in the ninth. ... New York OF Ichiro Suzuki doubled off third base for his 4,001st hit between the majors and Japan. ... Rodriguez was back in the lineup after a night off Wednesday. He got his second stolen base of the season. ... SS Derek Jeter (strained right calf) began a rehab assignment with Triple-A Scranton/Wilkes-Barre. ... RHP Hiroki Kuroda (11-8, 2.41 ERA), who leads the AL in ERA, faces Rays rookie Chris Archer (6-5, 2.95) on Friday night. ... Due to the long delay, the Yankees offered free seats for the Sept. 2-4 series against the Chicago White Sox to fans holding tickets for Thursday. ... Gibbons said CF Colby Rasmus, on the DL since Aug. 11 with a strained left abdominal muscle, will begin baseball activities Monday.Suggest a correction