Mark Trumbo also homered for the Halos, who handed Andy Pettitte (2-2) the loss in his 400th career start for the Yanks.
Haren (3-5) allowed one run on eight hits and struck out seven without issuing a single walk.
Pettitte went eight-plus innings, allowing five runs on nine hits, including Pujols' eighth home run of the season.
Pujols' two-run homer highlighted a three-run third inning that put the Angels ahead 3-0.
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