Haren (3-3) won his second straight start after losing three of his first four. He gave up a solo homer to Dan Uggla in the seventh and struck out four while throwing just 91 pitches.
Rafael Soriano came on in the ninth to pick up his ninth save.
Stephen Lombardozzi singled in Washington's first run in the opening inning and the Nationals then capitalized on an Atlanta error to produce two more in the second.
Kris Medlen (1-4) took the loss, giving up all three runs on seven hits with eight strikeouts over seven innings.
The teams split a four-game series with the Nationals winning the last two.