The former England captain, 32, opened the scoring after eight minutes and added a second-half penalty to take his tally in his debut MLS season to 12.
After two wins in their first 14 games, DC United have now gone nine matches unbeaten and won their past five.
DC sat bottom of the Eastern Conference when Rooney, Manchester United's record scorer, joined from Everton in June.
Read also:Rooney hits two as United beat Chicago
The club have now reached the MLS post-season for the first time since 2015 after climbing to fifth place.
They head into the final game of the regular season at Chicago Fire next Sunday with the chance of finishing as high as third in their division, which would clinch a home play-off match in the first round.
Rooney has been key to DC's resurgence, also contributing seven assists in his 19 appearances.
His first at Audi Field on Sunday came from a tap-in after Luciano Acosta pulled the ball back following a mazy run, before Rooney turned provider as Acosta curled home the second.
Rooney converted a penalty after Alex Ring handled the ball in the 74th minute.
Former Barcelona and Spain striker David Villa pulled a goal back for New York, who have one win in their past nine games.
Source: BBC