Rooney, who served a one-match suspension by missing D.C. United's game against Philadelphia Union, will now miss Saturday's match against Montreal Impact.
Rooney's red card against the Red Bulls came after VAR spotted the infraction, which the referee had not seen in a crowded penalty area at a corner kick.
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In his second season with D.C. United, Rooney will leave at the end of this campaign to join English Championship team Derby County as a player and assistant coach in January.
D.C. United have lost their past three matches and are fifth in the 12-team Eastern Conference with 39 points from 29 matches.
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