Rooney was given a red card for violent conduct after striking Red Bulls midfielder Cristian Casseres with a forearm during a penalty box collision.
The dismissal led to an automatic one-game suspension, which Rooney served last weekend when he sat out United’s game with Philadelphia Union.
However after reviewing the incident further, the MLS Disciplinary Committee on Tuesday confirmed Rooney had been given an extra game on top of his initial suspension.
The decision means Rooney will miss D.C. United’s trip to Montreal on August 31.
Rooney, 33, is in the final season of his 18-month MLS career after announcing earlier this month that he has signed for English Championship side Derby County as player-coach.
The former England and Manchester United star will join Derby from January 2020 at the conclusion of the MLS season.