Burnett (5-6) entered 5-0 in six career starts against Baltimore, but was booed off the mound during the Orioles' five-run fifth. He gave up a season-high eight runs in 4 1/3 innings and mockingly doffed his cap to the crowd as he walked off after being replaced by Brian Wolfe.
Manager Dave Trembley warned his players not to chase Burnett's breaking ball, urging them to take as many pitches as they could.
"If you go after first or second pitches you're playing right into his hands," Trembley said. "You don't really want to get two strikes on you because the guy has got devastating stuff. You just have to show a lot of patience with him, and you've got to be able to fight off good pitches with two strikes."
Burnett, who is winless in three starts, walked four and equaled a season worst by allowing 10 hits in his shortest outing of the season.
"You could tell he maybe got a little frustrated and was trying to split the plate a little bit more, coming right at guys and saying 'Hit it if you can,' " Payton said. "Fortunately, we were able to put some good swings on him."
Burnett apologized for mocking the crowd after he departed, saying it was "uncalled for."
"That's a mental mistake on my part," Burnett said. "I'm better than that. Obviously, from what we all saw, they every right to boo."
Guthrie (3-6) allowed one run and six hits to win for the first time since May 13 against Boston. He struck out six and walked none.
"It's good that he won the game because he means a lot to our club," Trembley said. "I don't care what the score is, or the situation, he'll give you what he's got."
Payton hit a two-run single in the third to give Baltimore a 3-1 lead, and the Orioles blew it open in the fifth. Payton had a three-run double with one out and scored on Guillermo Quiroz's double. Alex Cintron then singled to chase Burnett, who waved his cap as he headed back to the dugout amid a chorus of boos.
Brian Roberts capped the rally with a sacrifice fly off Wolfe.
"Our situational hitting was very good," Trembley said. "We got key hits when we needed them. Payton gave us a big lift today. Offensively, it was probably one of our better showings of the season."
Vernon Wells went 2-for-3 with an RBI in his return from the disabled list, but it wasn't enough to help the Blue Jays avoid their third straight loss.
"It was great to be back," Wells said. "Obviously, it didn't turn out like we wanted to but for the first day, everything checked out all right."
Wells was activated less than a month after he fractured his right wrist making a diving catch in a May 9 game at Cleveland. He started the game on the bench but came on as a defensive replacement after Shannon Stewart sprained his right ankle running out a grounder in the first.
Third baseman Aubrey Huff threw high and wide to first on the play and Stewart ducked to try to avoid the tag, but rolled his ankle on the side of the base and went down in pain. He stayed down and was treated by trainer George Poulis before walking gingerly off the field.
SS Freddie Bynum's error in the ninth was the Orioles' first since May 31, a span of 66 2/3 innings. ... Baltimore LHP Brian Burres, who has won just one of his past eight starts, will get an extra day of rest before his next outing, Friday against Pittsburgh. ... Besides Wells, the Blue Jays also activated INF John McDonald from the 15-day DL and recalled Wolfe from Triple-A Syracuse. To make room on the roster, Toronto placed 2B Aaron Hill (concussion) on the 15-day DL, designated RHP Armando Benitez for assignment and optioned INF/OF Joe Inglett to Syracuse.