The leaders had to weather a storm in the first half as goalkeeper Bill Hamid made some fine saves - the best from Bradley Wright-Phillips' downward header - and Tim Cahill hit a post.
But long balls from Hamid and Perry Kitchen allowed first Luis Silva and then Eddie Johnson to score second-half goals and lift DC to victory.
The Los Angeles Galaxy won their final game against rivals Chivas USA, who are set to be rebranded at the end of the season, 3-0.
Gyasi Zardes scored twice to push his claims for a United States call-up, with a Robbie Keane goal sandwiched in between.
The Galaxy now trail Western Conference leaders the Seattle Sounders by just two points.