Brett Cecil (6-2) pitched eight innings for Toronto, matching a career high. The left-hander allowed one run and five hits while improving to 4-0 with a 1.52 ERA in his past four starts.
Bautista led off the second with a drive off A.J. Burnett that went off the facing of the third deck in left, his career high 17th. He went deep again in the fourth, finding the same area again for a two-run shot.
Encarnacion led off the fifth with his eighth homer, a drive to left-center that gave Toronto a 4-0 lead.
Burnett (6-3) allowed six runs and six hits in six innings, walked four and struck out two against his old team. The right-hander had allowed just four homers in his first 11 starts this season and never more than one in a game.
Burnett has struggled in two starts in Toronto since opting out of his contract with the Blue Jays and signing with the Yankees after the 2008 season. He allowed five runs over 7 2-3 innings in a 5-1 loss to Roy Halladay on May 12, 2009.
Bautista leads the majors with 18 homers, and the Blue Jays have a major league-high 94 longballs.
Toronto added two more runs in the sixth. Bautista drew a leadoff walk and went to second on Alex Gonzalez's single before both runners moved up on a grounder. Bautista scored on a wild pitch and Gonzalez came home on John Buck's sacrifice fly.
Bautista, who also had a leadoff double in the eighth, went 3 for 3 with three RBIs.