Lee allowed one run and struck out seven in six innings. He escaped a first-inning jam by striking out the side, two coming after Kelly Johnson singled and Bautista doubled. He allowed a run in the fourth when Bautista doubled and scored on Adam Lind's single.
The Blue Jays also scored in the eighth, when Johnson doubled after Travis Snider reached on an error by centre fielder Scott Posednik.
Morrow, Carlos Villanueva, Darren Oliver and Jason Frasor limited the Phillies to four hits.