Howard put the Phillies in front for good with a solo blast in the second, then hit a two-run homer in the fourth. He also had a double in the eighth inning, raising his batting average to .339 with 11 homers and 29 RBI in his last 15 games.
Rain delayed the game almost two hours in the second inning, causing both starting pitchers to leave.
Philadelphia reliever Jamie Moyer worked 4 1/3 to get the win, allowing a run on four hits.
Brad Lidge, who has blown nine save opportunities this year, struck out one and threw only 12 pitches in the ninth to claim his 26th save.
Philadelphia increased its lead in the National League East to eight games over both Florida and Atlanta.
Although he faced only a 1-0 deficit when he left the game during the rain delay, Atlanta starter Tommy Hanson (9-3) took the loss.
Copyright 2009 by United Press International.