Visiting Chicago had taken a 51st-minute lead when Raheem Edwards danced his way through the D.C. backline and slotted past goalkeeper Bill Hamid.
However, former England and Manchester United captain Rooney – who also scored twice in the 5-0 rout of the Montreal Impact last time out – rallied his team and restored parity in the 62nd minute, clipping home from close range after his initial shot had been saved by Stefan Cleveland.
Though he soon let another golden opportunity pass, Rooney then maximum points for Ben Olsen's side nine minutes from time, lashing home from the spot after Luciano Acosta had been brought down inside the box.
While Sunday's win had no immediate impact on the playoff race, it was a massive boost to United's chances of earning one of the six spots in the Eastern Conference.
The club remains seventh in the East, two points off the sixth-placed Impact and seven points back of the Columbus Crew, with two games in hand on both sides.
Ben Olsen's side has now gone six matches without a loss, but D.C. still faces a tough closing run, though none of the teams the club will face in its final four matches have much left to play for.
Next up is Western Conference leader FC Dallas, where the primary motivation will be staying atop the conference standings, or at least in the top two to earn a first-round playoff bye, as the club has already secured a spot in the postseason.
A matchup with Toronto FC follows that, with TFC's playoff chase having come to an end on Saturday.
United will close out the season with a match against already-qualified New York City FC and another clash with the cellar-dwelling Fire.