The first came in the sixth, when Burnett, who carried a 3-0 lead into the sixth inning, allowed a two-out, two-run homer to Alex Rodriguez to cut the advantage to a run.
An inning later, Derek Jeter improved his American League MVP chances with a second two-out, two run homer to put the Yankees ahead for good.
The two teams would exchange three-run ninths, but the game was decided when Jeter swatted Burnett's 3-0 fastball into the seats in left-center.
"Two pitches, two pitches, that's it," Burnett said summing up just his third loss against six wins in his past nine starts. "They did what they are supposed to do with them.
"Two mistakes all night," Burnett said. "I had them where I wanted them, and it got away. Regardless of what happened after the seventh inning, I have to keep us in that game right there."
With the loss, Burnett fell back to even with an 8-8 record, but all things considered, the Jays have to be happier about their five-year investment in Burnett today than they were three months ago, when he had yet to show them much of anything two months into the season.
Burnett has two starts remaining, one Sunday against Boston and the other the following Friday in Yankee Stadium against New York.
REPLAY: Failed opportunities were the story of the Jays' 7-6 loss to the Yankees on Monday night.
With a red-hot A.J. Burnett matched up against Yankees rookie right-hander Darrell Rasner, the odds favored the Jays, and for five innings, that's the way it was shaping up.
Rasner was shaky over the first four frames, but somehow managed to get through allowing just three runs.
When the ever-patient Yankee hitters finally broke through against Burnett in the sixth and seventh with a pair of two-run homers, it was enough to turn things in their favor.
For the night, the Jays were a miserable 2-for-12 with runners in scoring position. The Yankees weren't much better at just 2-for-9, but in a one-run game, they didn't have to be.
NEWS, NOTES, QUOTES
--OF Reed Johnson established a career high for the number of times he has been hit by a pitch in a season in Monday's 7-6 loss to the Yankees. Johnson was hit for the 21st time (his previous was 20 in 2003) and extending his major league lead in that category.
--3B Troy Glaus broke out of his almost month-long funk in the ninth inning of Monday's game with a three-run homer. Glaus had not hit a home run since Aug. 21 in Oakland. The RBIs snapped a streak of 19 games without one.
--The sixth inning two-run homer by Alex Rodriguez Monday night snapped a string of 13 consecutive scoreless innings for Jays starter A.J. Burnett. Burnett has now logged at least seven innings in five consecutive starts and pitched six or more innings in nine consecutive.
--Brandon League gave up three runs, one of them earned, in the ninth inning of Monday's 7-6 loss to New York. League had not allowed an earned run in his past eight outings.
--OF Alex Rios was out of the starting lineup for the ninth consecutive game on Monday. Rios, however, did have his first at-bat since bruising a bone in his hand Sept. 8 in Anaheim. Rios pinch-hit for Frank Catalanotto in the ninth inning of Monday's 7-6 loss. He struck out.
BY THE NUMBERS: 0 -- The number of RBIs 3B Troy Glaus had totaled in September, through Sept. 17.
QUOTE TO NOTE: "He's been everything we expected and everything we wanted. And I think he's only going to get better." -- General manager J.P. Ricciardi, on the season of first baseman Lyle Overbay, who was acquired last offseason in a trade with Milwaukee.
RF Alex Rios was out of the starting lineup Sept. 9-18 because of a bruised right hand.
RHP Roy Halladay was hit in the right elbow by a line drive on Sept. 10. X-rays were negative, and he started on Sept. 15.
RHP Pete Walker went on the disabled list July 8 with a rotator cuff injury that required season-ending surgery. He was transferred to the 60-day disabled list on Sept. 5.