Josh Edgin (1-2) retired the first two batters in the Philadelphia ninth before issuing a walk to Chase Utley. Howard then hit his home run into the upper deck in right field.
Until Howard's long homer, the Phillies had managed only two hits -- one of them a first-inning home run by Jimmy Rollins.
The Phillies' comeback made a winner out of Jeremy Horst (2-0), who retired two batters in the eighth. Jonathan Papelbon came on in the New York ninth for his 36th save.
Cole Hamels started for Philadelphia and gave up two runs in six innings while striking out 10. He reached 200 strikeouts for the season.
New York lost its fourth game in a row. The Phillies, who began the night four games out of the second wild-card position in the National League, have won two straight.