The 28-year-old picked up the knock during Tuesday night's 1-1 draw against the reigning European champions.
He will definitely miss their visit to Newcastle United on Saturday and with fellow forward Robin van Persie already on the sidelines, this latest news will be a major headache for manager David Moyes.
The club posted on Twitter on Friday evening: "Confirmed: Wayne Rooney set to miss @NUFC vs #mufc, may be doubtful for Bayern trip."
Moyes told MUTV: "He's got a badly bruised toe. He's got a terrible toe. Not only is it a problem for this game, it could be a problem for the Munich match.
"We need to monitor it. We'll get him treatment all over the weekend and see if we can speed it up."
Although Rooney has only scored two Champions League goals this season, he would be sorely missed if he was unavailable for a second leg in which United must score to progress.
With Dutchman Van Persie out with a knee injury, Danny Welbeck and Javier Hernandez have only been used sparingly this term.
All those associated with Old Trafford will be desperate for a swift recovery for the England striker, as happened four years ago against the same team.
Sir Alex Ferguson ruled Rooney out of the second leg of United's Champions League quarter-final against Bayern in 2010 after he suffered an ankle injury in the first leg.
The former Everton striker then made an incredible recovery to start the second leg at Old Trafford, but was still unable to to prevent United going out of the competition on away goals.