Former England and Manchester United star Rooney was shown a red card on 52 minutes after a dangerous, studs-up tackle on LAFC's Uruguayan striker Diego Rossi, who would go on to complete a clinical hat-trick.
Referee Robert Sibiga initially looked to have given Rooney a reprieve, brandishing only a yellow card for the tackle.
But after consulting the Video Assistant Referee, Sibiga changed the yellow to red, leaving United skipper Rooney to trudge off the field without protest.
"Yeah I think it was a red card," Rooney said after the game. "I've lunged. I tried to win the ball, and I've caught the player. I have no arguments."
Rooney's red completed a miserable afternoon for D.C. United, who by that stage were trailing 3-0 against a vastly superior LAFC side.
The eagerly anticipated battle between the leading teams in the Eastern Conference and Western Conference turned into a one-sided affair at Washington's Audi Field, with Los Angeles ruthlessly exploiting some sloppy play from the home side.
The game was effectively over in little more than half an hour, with Los Angeles surging into a 3-0 lead thanks to two goals from Rossi and a curling effort from Mexico international Carlos Vela.
United had been under pressure from the outset, and were fortunate not to have gone a goal down after only nine minutes when Leonardo Jara was adjudged to have handled in the area to concede a penalty.
Vela stepped up for the spot-kick but was thwarted by a fine block from United goalkeeper Bill Hamid. Vela's attempted follow-up from the rebound hit a post.
Los Angeles did not have long to wait for the opener, however, and in the 16th minute Vela made amends with the game's opening goal.
A mix-up in midfield saw D.C. United cough up possession cheaply, allowing Adama Diomande to thread a pass through to Vela, who coolly took his time before placing a curling shot beyond Hamid.
Vela turned creator for LAFC's second, picking out Rossi with a delightful low cross with the outside of his left foot allowing the Uruguayan to jab home the finish for 2-0.
Rossi added his second in the 32nd minute, capitalizing on good work from Mark Anthony Kaye to curl in a superb right-foot finish to all but seal the win.
Rooney's dismissal early in the second half snuffed out any faint hope of a comeback, and Rossi duly added insult to injury by completing his hat-trick to make it 4-0 on 76 minutes.
LAFC moved four points clear of Los Angeles Galaxy at the top of the Western Conference, with 16 points from six games.