The England striker, who damaged ligaments in his right ankle in the first leg against Bayern last week and was expected to be missing for three weeks, lasted 55 minutes before going off with more damage to the joint.
NEWS:Robben volley rips up Rooney script
"He has a burst blood vessel just below the ankle joint," United manager Sir Alex Ferguson, told reporters. "He won't be out for too long. It was never a serious injury.
"The fact is he was unlucky because he went over on it again. He had a couple of challenges on it and I don't think he got much protection."
Earlier this week Ferguson said that Rooney, who has scored 34 goals this season, had virtually no chance of playing against Bayern but with a 2-1 deficit to overturn and the player making a quick recovery he decided to start with him.
For 41 minutes it looked like an inspired decision as Bayern appeared completely distracted by Rooney's presence, falling 3-0 behind on the night with Darron Gibson and Nani scoring.
However, the gamble began to misfire as Rooney was substituted and United were pole-axed by Arjen Robben's stunning volley which hauled Bayern back to 2-3 on the night and sent them through on the away goals rule.
NEWS:Robben stunner sends Bayern through
Ferguson denied that he had rushed Rooney back into action too early - a decision that could have implications for United's final five games of the season as they try and win a fourth consecutive Premier League title.
"He had a training session on Tuesday and was very impressive," Ferguson said. "He did everything that I could ask of him and had an intensive examination. There was no risk, he was just unlucky."
Rooney, who missed United's costly 2-1 home defeat by Chelsea in the Premier League on Saturday, is now unlikely to play against Blackburn Rovers this weekend.
His injury caused widespread concern in England, with even British Prime Minister Gordon Brown referring to it, because Rooney's fitness is seen as vital to England having a successful World Cup in South Africa.
