Hernandez (5-1) gave up four hits.
David Wright was 2-for-3 with a double and an RBI, while Daniel Murphy also had two hits and drove in a run for the Mets. Outfielder Ryan Church (hamstring) was activated from the 15-day disabled list prior to the game and had two hits and a run.
Adam Dunn had two of the five hits for Washington, which has lost four of its last five games.
Craig Stammen (0-2) suffered the loss in only his fourth big league start. He allowed five runs on six hits in five innings.