Werth's shot in the fifth inning erased a 1-0 deficit for the Nationals, who beat the Phillies for the seventh straight time dating back to last season.
Chad Tracy chipped in with a two-run clout and Ian Desmond added a solo shot as the Nationals won their fourth straight overall and clinched their three-game set with Philadelphia.
Gonzalez (3-1) yielded just one run over seven innings, surrendering four hits with a walk and seven strikeouts.
Phils starter Vance Worley (2-2) was roughed up for five runs on 11 hits over six innings.
Philadelphia dropped its third game in four tries.