Rooney suffered minor ligament damage to his right ankle in the first leg against Bayern in the Allianz Arena, and initial reports said he could be out for up to a month.
But speculation in the press had suggested that Sir Alex would risk him against Bayern in a bid to reach the Champions League semi-finals. On Monday it was reported that the 34-goal striker had a 40% chance of featuring in the return leg.
Sir Alex has now said he is not prepared to risk the long-term fitness of the England international as United look to overturn a 2-1 deficit.
''He's got no chance,'' he said. ''We've made some good progress with the lad, the medical team have done fantastic, but I'm not prepared to take a risk on a player who is not 100% fit.
''The boy is making good progress. The medical team have done a fantastic job but it is an ankle injury the same as any other ankle injury. You can't take a risk with a player who is not 100%.
''I don't think he will be on the bench although he might talk me into it, it is a difficult one.''
The one piece of good news for Ferguson is the likely availability of John O'Shea, who has not played since suffering complications in his recovery from a dead leg sustained in the Republic of Ireland's World Cup play-off defeat to France in November.