Ryan Church, Dmitri Young and Chris Snelling all hit home runs, with Church extending his hitting streak to 11 games. Snelling drove in three runs, and Brian Schneider had two runs and three hits as the Nationals rose to 3-9 for the season.
Hill walked one batter and struck out five.
Jose Valentin and Shawn Green hit RBI doubles for the Mets, who have split their last four.
Losing pitcher Orlando Hernandez (1-1) gave up six earned runs and eight hits in five innings. He was ejected in the sixth after hitting Hill following Snelling's two-run homer.
Mets third baseman David Wright singled in the second to extend his hitting streak to 23 games.