Alex Rodriguez sat out because of a bruised calf, a night after getting hit by a pitch from Josh Towers. In that game, Roger Clemens and manager Joe Torre were ejected after Clemens apparently retaliated by hitting Alex Rios.
"My guess is, with the off day tomorrow, he'll be all right," Torre said of Rodriguez, who declined to speak after the game, jogging away from a crowd of reporters toward the team bus.
The Yankees are off Thursday before opening a three-game series at Cleveland on Friday. New York plays 17 of its next 20 games against teams currently in playoff positions.
After Tuesday's hijinks, Wednesday was a much calmer game. Frank Thomas added three RBI for the Blue Jays, who have won nine of their past 11 at home.
Wells finished 3-for-4 and scored twice as Toronto matched a franchise high with nine doubles.
"It's the right way to react to what happened," Wells said. "Anytime you can do that after a loss like (yesterday) is huge. That's what you have to do in a situation like this when you're playing one of your rivals and you need a big win."
After Cleveland, the Yankees return home for three with Baltimore and four with Detroit, then head west for three games against the Los Angeles Angels and four games at Detroit. After that, it's home again for a three-game series with Boston.
New York has gone 20-8 since the all star break. Twenty-five of those games came against teams with losing records.
"If we keep playing the way that we are it could be a very fun October," outfielder Johnny Damon said.
"We have some momentum. We have some guys swinging very hot bats now," he added. "We're feeling pretty good about our chances."
Halladay (13-5) gave up four runs and six hits over seven innings and walked just one. He improved to 10-4 in his career against the Yankees.
"You realize what a good team they are and you're not always going to stick it to them," Halladay said. "Every once in a while it's a nice feeling."
Chien-Ming Wang (13-6) allowed a career-high eight runs and nine hits over 2 2/3 innings, his shortest career outing, and lost for the first time in four starts. He walked two and struck out three.
"Everything was down the middle," said Wang, who had allowed seven runs three times previously. It last happened on May 10 against Texas.
Torre said Wang's pitches were moving laterally but not sinking as much as normal, leading to control problems.
"He was getting behind in some counts, which was uncharacteristic," Torre said.
Toronto took a 3-0 lead in the first on an RBI double by Rios and a two-run single by Wells.
Cano closed the gap with a two-run homer off Halladay in the third before Toronto blew the game open with a five-run third, one of two innings in which the Blue Jays batted around.
Matt Stairs led off with a double and scored on Lyle Overbay's single. One out later, Wells doubled home Overbay and scored on Thomas' single. Troy Glaus walked and Aaron Hill grounded out before Gregg Zaun chased Wang with a two-run double down the right-field line.
Stairs walked, Overbay doubled and Rios reached on Derek Jeter's fielding error, loading the bases for Wells, who hit a sacrifice fly. Thomas flied out and Glaus walked before Hill and John McDonald sandwiched two-run singles around a walk to Zaun.
Cano and Matsui both homered off Halladay in the seventh. Matsui's homer was the 101st of his career, the most by a Japanese-born player in major league history.
Yankees outfielder Bobby Abreu was ejected by home-plate umpire Derryl Cousins for arguing a called third strike in the fourth inning. It was Abreu's first ejection of the season.
"It was a bad pitch low and in and I discussed that," Abreu said. "He didn't like the way I slammed the bat in the dugout and he just threw me out."
Torre said Cousins was too quick to toss Abreu, who was replaced by Shelley Duncan.
"The fuse was a little short," he said.
- Glaus, who is stuck in an 0-for-21 slump, was the only Blue Jays starter not to record a hit. He walked and scored twice.
- Melky Cabrera extended his hitting streak to a career-high 14 games with an infield single in the sixth.
- Stairs doubled in his first two at-bats to give him five consecutive doubles. He's the first major leaguer to accomplish the feat since Colorado's Charles Johnson did it in 2004.