One week on from the fury at Chelsea's home clash with Burnley, referee Roger East was at the centre of an alleged case of mistaken identity at Old Trafford.
Rooney scored from a penalty after 66 minutes when Radamel Falcao was fouled by John O'Shea and referee East sent off Wes Brown, instead of O'Shea, leaving the visitors to struggle on with 10 men. Ironically, both defenders are former United players.
O'Shea, who clearly pulled Falcao back as he was about to shoot, pleaded with East to send him off instead, but Brown was shown the red card and walked.
East explained later, in a statement issued by the referees' body that he believed he saw both players make contact with Falcao, but added that none of the officials at the match offered any guidance.
Rooney scored his second six minutes from time to ensure victory and lift United back to third in the Premier League behind leader Chelsea and second-placed defending champion Manchester City, both of whom did not play Saturday.
Chelsea meets Tottenham Hotspur in the English League Cup final on Sunday when City visits Liverpool and Arsenal hosts Everton in the Premier League.
Saturday's win confirmed United's challenge for a return to the Champions League on a day when Southampton, the only other top team in action, was beaten 1-0 by improving West Bromwich Albion.
West Ham United's fading bid for a place in Europe was hit in the day's early fixture when it lost 3-1 at home to Crystal Palace while Swansea won 1-0 at Burnley, Newcastle beat struggling Aston Villa, under the new management of Tim Sherwood, 1-0 and Stoke overcame Hull also by one goal.
In all, four of the six Saturday fixtures produced just a single goal and, and for the second consecutive week, a key refereeing decision became the chief talking point.
Referee East spoke to his assistants at Old Trafford before he confirmed his decision to send off Brown. The fourth official at the game was Martin Atkinson who was the referee in charge when Chelsea drew 1-1 with Burnley a week earlier, an encounter that was also engulfed in controversy about his decision-making with Chelsea manager Jose Mourinho citing four questionable incidents.
Two hours after the match, the Professional Game Match Officials Limited (PGMOL) issued a statement which explained East's actions.
"From his position Roger East, the match referee, believed he saw contact from John O'Shea and Wes Brown on Radamel Falcao," said the statement. "As he thought Brown made a foul on Falcao, while he was in the act of shooting, he dismissed Brown. After the incident, the match referee consulted with his team of officials, but none were better placed to offer guidance."
Sunderland manager Gus Poyet said: "It was difficult to see what happened - we're trying to get a video. It's between two players. We have to analyze it. It didn't look an easy decision to make. The referee said that Wes Brown was the one who fouled Falcao first... That's what he told the players."
United manager Louis Van Gaal said he was happy with his team's response in the second half after a dull opening period. "I think the first half could be better, but the second half we controlled the match. I'm very pleased," he said.
"The players protested because they felt the wrong player was sent off. That's a mistake. You make mistakes as well -- and so do I. It can happen."
He was also defensive about his decision to withdraw Argentine winger Angel di Maria at halftime and replace him with Belgian youngster Adnan Januzaj. "I want to win," he said. "I have to observe and analyze. We were better in the second half so I cannot say it was the wrong decision. We have to give him time to adapt and lift his confidence again. He's a human being and makes mistakes like everyone else."
West Brom manager Tony Pulis said striker Saido Berahino, who netted his 17th goal of the season after only 71 seconds, had scored "a goal that top, top class players score and Berahino could be a top, top class player. Since I came to the club, there has been no doubt about his ability. He just needs direction."
His joy, at beating Southampton for the first time as a manager in four attempts, was in contrast to Ronald Koeman's dismay after his team's toothless display. "We lack confidence," he said. "But we will keep going and we must beat Crystal Palace on Tuesday."