Jason Giambi spoiled Burnett's shutout bid with a solo home run in the ninth, his 19th. Jorge Posada followed with a single before B.J. Ryan replaced Burnett. Ryan got Robinson Cano to ground into a double play to record his 18th save in 20 opportunities.
The Yankees ended the first half of the year by losing three of four against the Pirates and Blue Jays. New York's 50-45 record is an improvement on a year ago, when they went to the All-Star game at .500.
Toronto won for the fifth time in six games to improve to 47-48 at the break.
Burnett, who has won four of his past five, improved to 5-2 in eight career starts against New York.
The Yankees did little else to threaten Burnett. Bobby Abreu doubled to begin the fourth and, two outs later, Posada was hit by a pitch, but Cano grounded out to first.
Abreu and Alex Rodriguez had back-to-back one-out singles in the sixth, but Giambi flied out and Posada struck out.
Yankees left-hander Andy Pettitte came in having won seven of his past eight decisions, but took the loss in this one after allowing four runs and eight hits in six innings. Pettitte (10-7) walked one and struck out six.
All the scoring came in the second, when Kevin Mench led off with a double and scored on a single by Scott Rolen. Adam Lind walked before Scutaro drilled a 1-2 pitch over the wall in left for his third homer of the season.
Rolen doubled to begin the fourth and went to third on Lind's single, but was thrown out at the plate by Abreu when he tried to score on Scutaro's fly to right.
Toronto finished with four doubles in all, and five of the Blue Jays' nine hits were for extra bases.
Derek Jeter batted in the leadoff spot for the second straight game and finished 0-for-4 with two strikeouts, snapping a 10-game hitting streak. Manager Joe Girardi said Jeter will continue to lead off until OF Johnny Damon (left shoulder) returns from the disabled list. Damon is eligible to come off the DL next Sunday.
Posada caught for the second time in three games but surrendered two stolen bases. Posada, who missed 32 games with a right shoulder injury earlier this season, has thrown out just three of 35 runners.
