The slumping Pujols, who had signed a 10-year, $240 million contract with the Angels during the off-season, was given the night off Saturday after going just 2-for-27 in his previous 18 contests.
The slugger had gone 139 at-bats without hitting a homer before belting a 2-2 pitch from Drew Hutchison (1-1) into the Angels' bullpen in left field, putting Los Angeles ahead 4-1 in the fourth inning.
Mark Trumbo and Alberto Callaspo each added an RBI as the Angels earned a split in their four-game set with the Blue Jays.
Jerome Williams (3-1) yielded three runs (two earned) on eight hits over 6 2/3 innings to record the victory.
Hutchison surrendered four runs on eight hits in a 5 1/3-inning effort for Toronto.