Rooney picked up the knock during Tuesday night's 1-1 draw against Bayern in the first leg of the quarter-final tie at Old Trafford.
The problem has ruled the England striker out of United's Premier League game against Newcastle on Saturday, and he is now a doubt for Wednesday's return leg in Germany.
The club posted on Twitter on Friday evening: "Confirmed: Wayne Rooney set to miss @NUFC vs #mufc, may be doubtful for Bayern trip."
United added that manager David Moyes had 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.
Robin van Persie is already out because of a knee injury, while Danny Welbeck and Javier Hernandez have only been used sparingly this term.
The revelation that the 28-year-old is carrying the injury could, of course, just be a ploy to wind up Bayern, who have the ascendancy in the tie following Bastian Schweinsteiger's away goal.
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 a near-miraculous recovery to start the second leg at Old Trafford, but he could not prevent United going out of the competition on away goals.