The England striker hadn't been expected to feature against Bayern as he had missed the previous match against Chelsea with the injury, but Ferguson gambled on his fitness, only to see his star player suffer another setback.
However, Rooney has returned to training this week and Ferguson admitted the 24-year-old will be in the squad to face City if he suffers no reaction.
"He has done some work over the last couple of days and we will see how he is for Saturday's game," said Ferguson, who also confirmed Ryan Giggs and Rio Ferdinand have an outside chance of being involved at Eastlands.
Reports in England on Friday claimed Rooney will be the target of a big-money bid from Real Madrid in the close-season as the Spanish club look to reunite the striker with former United team-mate Cristiano Ronaldo, who moved to the Bernabeu last year.
It has been suggested United would find it hard to turn down a substantial offer for Rooney as they have amassed huge debts under the ownership of the Glazer family.
But Ferguson was quick to brush off the reports. "It is the silly season isn't it," he said. "It always happens at the end of the season. Wayne Rooney will still be here next year."
Ferguson was more interested in focusing on Saturday's crucial clash with City as the champions try to keep their title hopes alive.
United are four points behind leaders Chelsea with four games to play, while City are firmly in the hunt for a top-four finish and the Champions League place that comes with it.
"It is the most significant derby for a long time," Ferguson said. "City and Spurs are trying to get into the Champions League for the first time in their history.
"It is the first time since I have been manager that we are facing City when they have a genuine chance of achieving something."
Ferguson was also boosted by the news that England midfielder Owen Hargreaves is set to be included for the City game, giving him the chance to make his first senior appearance in almost 20 months after a series of knee operations.
Source: AFP European Edition