Rooney had not been ejected from a Premier League match since receiving two yellow cards against Fulham on March 21, 2009.
The win was just United's second in seven matches under new manager Louis van Gaal.
Meanwhile, Manchester City threw away an early two-goal lead before recovering to beat Hull 4-2 for its first win in four Premier League matches.
Edin Dzeko scored twice and Frank Lampard grabbed his fourth goal in three games.
City looked to have sealed the points early on at KC Stadium as Sergio Aguero and Dzeko both found the net inside 11 minutes, with Dzeko hitting a stunning strike from the edge of the penalty area.
Frank Lampard celebrates after scoring for Manchester City. Photo / Getty Images
But City let Hull back into the match after center back Eliaquim Mangala headed an own-goal past Willy Cabellero, who replaced the dropped Joe Hart.
Abel Hernandez then converted a penalty kick after being recklessly tackled high by Mangala.
In London, Diego Costa scored his eighth goal in six Premier League games to help give Chelsea a 3-0 win over Aston Villa and consolidate top spot in the standings.
Costa headed in the second goal in the 59th minute after Oscar had put Chelsea ahead in the seventh minute at Stamford Bridge.
Diego Costa has scored eight goals for Chelsea this season. Photo / Getty Images
Brazilian midfielder Willian rounded off the win in the 79th as Chelsea bounced back from conceding Frank Lampard's late equaliser against Manchester City last weekend.
It was Chelsea's fifth win to go with the draw at City, putting it three points clear of Southampton atop of the standings with 16 points.
It was Villa's second straight loss after a great start to the season, with Paul Lambert's side remaining on 10 points.
In the day's late game, Alex Oxlade-Chamberlain's second-half equaliser gave Arsenal a 1-1 draw against Tottenham.
Spurs forward Erik Lamela failed to clear in the 74th minute and the ball ricocheted around the penalty area before falling to Oxlade-Chamberlain, who lashed the ball in from close range. Lamela put his face in his hands after the goal in the London derby.
Tottenham went ahead in the 56th when Nacer Chadli scored after Arsenal midfielder Mathieu Flamini lost possession. The ball was collected by Christian Eriksen, who laid it off to Lamela. His throughball split open the Arsenal defense and Chadli slotted the ball into the bottom left corner.
Chadli was later booked for antagonising Arsenal fans with his goal celebration.
- AP
