The former England captain bent a glorious effort over the wall and into the top corner in the 18th minute, his 10th goal of the Major League Soccer season.
Victory strengthened DC United's hold on a play-off spot in the Eastern Conference – they lie sixth, having taken 47 points from 32 matches played.
Rooney has blossomed since joining DC United from Everton in June, registering six assists in addition to his 10 goals in 18 MLS appearances.
His impressive form has earned himself a place on the list of nominees for the Most Valuable Player award alongside LA Galaxy forward Zlatan Ibrahimovic, New York Red Bulls striker Bradley Wright-Phillips and New York City FC star David Villa.
“I think so far he did fantastic, he changed the team he came to and they have done good results,” Ibrahimovic said of Rooney in an interview with Sky Sports News.
Rooney fired in the winner (USA TODAY Sports)
“Before he came it was different results, but he has been playing good and scoring goals and he shows that he is Rooney.
“I don't need to describe Rooney. Everybody knows Rooney and they know his quality, so it's only for him to play the games and perform.”
In the Western Conference, Sporting Kansas City scored four times inside the final half-hour to come from 1-0 down to win 4-1 on the road against the Vancouver Whitecaps, whose play-off hopes now hang by a thread.
Trailing to Felipe's 43rd-minute goal, the visitors levelled through Yohan Croizet before Daniel Salloi put them ahead eight minutes from time.
At the death Gianluca Busio added a third and Salloi made it four.
The Seattle Sounders also won away, triumphing 2-1 at Orlando City to seal their place in the play-offs.
Goals from Victor Rodriguez and Handwalla Bwana had them two up after only 13 minutes, with Dominic Dwyer pulling one back in the second half for the hosts.