United, who were bottom of the table when Rooney joined in June, are seventh in the Eastern Conference of the MLS.
They are two points behind Montreal Impact with two games in hand, with the top six qualifying for the play-offs.
Rooney levelled against former Manchester United team-mate Bastian Schweinsteiger's side and then struck the winner from the penalty spot.
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DC United had won only two of their first 12 games before Rooney's arrival but have now scored 55 goals, their highest league tally since 2007.