Bautista hit the second pitch from Phillies starter Cole Hamels for a home run to center field, then added a pair of doubles in his big afternoon.
The Phillies tagged Toronto reliever David Purcey for two runs in the sixth, the first on Tyson Gillies' home run, and Jesse Carlson for three more runs in the seventh.
Right-hander Brandon Morrow, acquired by the Blue Jays in a trade with Seattle, pitched two hitless innings in his first bid to become part of their starting rotation.
Phillies reliever J.C. Ramirez gave up four runs on five hits in 1 1-3 innings.
