The Phillies improved to 5-0 in Atlanta this season
Howard's homer gave Philadelphia a 4-0 lead in the third and Adam Eaton (3-6) lasted five innings to get the victory, allowing two runs on five hits.
Philadelphia took a four-run lead into the bottom of the ninth, but had to survive a scare brought on by Howard's two fielding errors in the inning.
The miscues allowed the Braves to load the bases with two away. Mark Teixeira then hit a long shot that barely went foul and he eventually struck out swinging against Brad Lidge to end the game.
Jorge Campillo (3-3) took the loss, giving up five runs on eight hits in five innings.
Atlanta has dropped four in a row and six out of eight.