Howard's miserable season had already cost him his cleanup spot in the order, and he entered the game batting .189. Howard hit a two-run homer on Friday and a three-run shot in the first inning against Trevor Cahill (0-3) on Sunday.
Howard, who once hit 45 or more homers in a season for four straight years, has all three of his homers in the last five games and bumped his average up to .193
Jonathan Papelbon had his fourth save. He allowed Alberto Callaspo's pinch-hit solo homer in the ninth.
Ben Revere knocked in the go-ahead run with a triple and the Phillies won two of three games in the series.
Jerome Williams (2-1) allowed three runs and eight hits in 6 2-3 innings for the Phillies.