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Ferguson said on Tuesday that he was "not prepared" to risk Rooney's ankle injury on Wednesday against Bayern, who won the first leg 2-1 in Munich last week.
Rooney opened the scoring for United last week but suffered ankle ligament damage after landing awkwardly on his ankle in the final minute of play.
He was expected to be out of action for two to three weeks. However recent reports claimed the England international had responded well to treatment, giving fans hope that he could make a shock return to the United bench for the decider against Bayern.
United boss Sir Alex Ferguson has said he would not risk using Rooney if he was not 100% fit, and reports late on Sunday said the club's medical staff had given the striker only a 40% chance of playing.
In Rooney's absence United suffered a 2-1 defeat to Premier League title rivals Chelsea at Old Trafford on Saturday.
