Alex Rios, Scott Rolen and Adam Lind each drove in a run for Toronto, which got its first win against a National League team in seven tries this season.
The Blue Jays loaded the bases five times in the game but were 4-for-19 with runners in the scoring position and stranded 16 men.
Toronto's Lyle Overbay tied the score at 3-3 in the ninth on a bases-loaded walk.
Toronto starter Ricky Romero allowed three runs on six hits with two walks and nine strikeouts over seven innings. Scott Downs (1-0) earned the win with a scoreless ninth.
Jayson Werth hit a two-run homer for the Phillies, who have lost six of 10. Chase Utley was 3-for-4 with a walk and drove in the Phillies' other run.
Copyright 2009 by United Press International.