One of Howard's hits was a solo home run in the top of the second, one of three round-trippers Philadelphia hit in the contest. The others were a two-run blast by Pat Burrell in the third and a solo shot by Jimmy Rollins in the fifth.
Chase Utley drove in a run, while both he and Rollins had two hits, as the Phillies won for the seventh time in their last 10 games.
Winner Adam Eaton (10-9) yielded three earned runs and five hits in five innings.
Closer Brett Myers recorded his 19th save.
The losing pitcher was starter Shawn Hill (4-5).