"It's disappointing," manager Joe Torre said. "They shut us down offensively."
The Yankees, who fell 5½ games behind the first-place Red Sox in the AL East, now will go to Fenway Park to begin a big three-game series against their longtime rivals Friday night.
Roger Clemens threw 40 pitches in a bullpen session Thursday and said he has "no doubt" he'll be able to return from a sore elbow to start the series finale Sunday night.
"We know we have something at stake going into Boston. We know we have to play well," Johnny Damon said. "There's a lot of things that can happen at Fenway Park. Hopefully, it's good for us and not so good for them."
Damon hit a home run and rookie Ian Kennedy allowed one hit in seven-plus innings for New York, which leads the wild-card race by 3½ games over Detroit.
"Kennedy was remarkable, absolutely remarkable," Torre said. "He was so good, pitch count-wise. What a great start for this kid. He went about his business like he's been in the big leagues for 10 years."
Still, the Blue Jays (73-73) managed to end a five-game skid. They lost 5-4 to Tampa Bay on B.J. Upton's ninth-inning home run last Saturday, then 5-4 to Detroit on Monday when the Tigers rallied for four in the ninth.
"We needed a win," Thomas said. "It's been two walkoffs against us in the past five days."
New York came close to taking the lead in the ninth after Bobby Abreu led off with a single against reliever Casey Janssen. Alex Rodriguez struck out. Left-hander Scott Downs (3-2) replaced Janssen, then gave up an infield single to Hideki Matsui.
Damon provided a light moment in the sixth, retiring Rios on a fly ball for the final out, then giving the ball to a fan seated in the front row in left. The fan responded by giving Damon a $20 bill. Damon took the money, ran further down the line, then handed the bill to a young child.
"Hopefully, the fans that hated me have a newfound respect for me," Damon said. "They were on me. I figured I might as well take $20 and give it to a kid, you know? Hopefully he can go out and buy a Yankee hat."
Speaking through a chain-link portion of the outfield fence, Damon appeared to recount the story to Toronto's relievers in the bullpen when he returned to the field in the bottom of the seventh.
Making his third major league start, Kennedy left after Gregg Zaun walked to begin the eighth. The right-hander walked four and struck out seven, both season highs, and lowered his ERA to 1.89.
Toronto opened the scoring in the first when Thomas doubled home Adams, who had walked.
"That was probably (Kennedy's) only mistake, a fastball over the plate," Yankees catcher Jose Molina said.
Kennedy responded by retiring the next 15 batters, a streak that ended when Adams drew a two-out walk in the sixth.
"They're a good fastball-hitting team," Kennedy said. "I tried throwing changeups and curveballs, changing their eye levels a little bit with fastballs. That's what I've got to do. I don't throw like Burnett, throw 97, 98 (mph)."
Damon tied the score at 1 in the sixth with a home run into the second deck in right. Derek Jeter followed with a single and Abreu walked, but Burnett caught Rodriguez looking at a 99 mph fastball, then got Matsui to line out sharply to first.
"It seems like every time he pitches, he's pretty good," Damon said. "You never have a comfortable at-bat. Tonight he was spotting his fastball inside and out, up and down. His curveball is one of the best around, also."
Burnett allowed one run and four hits with eight strikeouts and two walks. He has won only once in his past five starts.
"I was trying to attack them and give them a look at everything I have every at-bat, keep them guessing a little bit," Burnett said. "It takes a lot out of you, pitching against that team."
- Blue Jays OF Vernon Wells was held out of the starting lineup, but entered as a defensive replacement in the ninth. Wells, who will undergo surgery at the end of the season to remove a cyst from his left shoulder, is batting .149 (7-for-47) in September.
- LHP Andy Pettitte left Toronto on Thursday to travel to Boston, where he'll pitch against Red Sox RHP Daisuke Matsuzaka in the series opener Friday.