The victory completed a three-game sweep at Nationals Park and was payback for a similar sweep by Cincinnati at the Great American Ballpark in July.
Austin Kearns had three hits and Emilio Bonifacio two in the Nationals' third straight win following a nine-game losing streak.
Winner Collin Balester (2-3) yielded an earned run and six hits in 5 1/3 innings with two walks and five strikeouts.
Joel Hanrahan earned his first save.
Cincinnati scored on solo homers by Joey Votto and Corey Patterson.
Votto had three hits and Patterson two in the Reds' eighth loss in their last nine games.
The losing pitcher was Johnny Cueto (7-11).