Cole Hamels (3-2) gave up six runs and eight hits in six innings for the win. He struck out seven in his worst start this season since allowing seven against Colorado to open the season.
Brad Lidge pitched a scoreless ninth for his 11th save.
Shairon Martis (5-1) lost for the first time in 10 starts for Washington. He surrendered seven runs and seven hits in four innings. Howard has plagued Martis in his career hitting three homers and driving in nine runs in seven at-bats.
Jimmy Rollins and Shane Victorino also had a pair of hits for the Phillies, who improved to 9-2 against the Nationals this season while dealing Washington its fifth straight loss.
Washington got a run back in the fourth on Alberto Gonzalez's RBI triple that scored Austin Kearns to pull within 6-4, but Hamels delivered an RBI double to restore Philadelphia's three-run lead.
Pinch-hitter Ronnie Belliard hit a two-run homer to left in the sixth to pull Washington to 7-6. But Philadelphia tacked on a pair of runs in the bottom of the inning when Anderson Hernandez booted Howard's grounder to second with the bases loaded.
The Nationals took a 3-0 lead in the second with three hits, as Will Nieves drove in two with a double and Hernandez one with a single.
Notes: Prior to the game, the Nationals recalled Gonzalez from Triple-A Syracuse and optioned outfielder Justin Maxwell to Syracuse. Gonzalez, who batted .311 in 23 games with Syracuse, went 2-for-3 with a run and an RBI Saturday. Gonzalez was filling in at shortstop for Cristian Guzman, who got the night off to rest a jammed right thumb. Chase Utley was hit by a pitch in the eighth inning, his major league leading 11th hit by pitch this season. Washington right fielder Adam Dunn committed two errors, giving him seven for the season.
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