The England striker tapped in newly crowned FIFA Player of the Year Cristiano Ronaldo´s low cross from three yards out after only 56 seconds, but he was forced off the pitch at Old Trafford with a hamstring injury about five minutes later.
"With a hamstring you are talking a minimum of three weeks (out)," United manager Sir Alex Ferguson said. "We hope it isn´t any longer than that."
"Wigan are the best side that has played here this season by far," Ferguson said praising the Latics’ resilience. "It was an outstanding performance from them. They really made us work."
Carlos Tevez, who replaced Rooney, and center back Jonny Evans, already playing in place of the injured Rio Ferdinand, completed the game despite taking heavy knocks during the first half.
With a game in hand, United was two points behind Liverpool, which has 46 points. United could go to the top of the standings by beating Bolton on Saturday a day ahead of the Merseyside derby.
Chelsea, which dropped to third place with 42 points, played in the FA Cup and conceded an early goal at League One team Southend in a third-round replay before recovering to win 4-1.
In other replays, Hull beat Newcastle 1-0 and Crystal Palace edged Leicester 1-0.
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