Both homers came in the fifth inning off Justin Lehr.
Scott Campbell added a bases-clearing triple in the eighth inning for the Blue Jays.
Jimmy Rollins and Greg Dobbs each drove in a run for Philadelphia.
Both starters pitched a pair of scoreless innings.
Toronto's Scott Richmond struck out a batter in his two innings, while Carlos Carrasco fanned three in his outing for the reigning World Champions.
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