Marlon Byrd hit a two-run homer and Jimmy Rollins hit a solo shot to back Kyle Kendrick (7-11). The right-hander allowed four runs and seven hits in six innings.
The last-place Phillies went 7-2 on their best homestand this season.
Denard Span was 3 for 4 and fell a triple short of the cycle for the Nationals. Doug Fister (12-5) allowed a season-high 10 hits and five runs - four earned - in 5 2-3 innings.
The Nationals had won 12 of 13 before losing three in a row in Philadelphia. They still have the best record (75-57) in the NL and a comfortable 6½-game lead over Atlanta in the division.