The 24 year-old is almost certain to miss Saturday's table-topping clash with Chelsea at Old Trafford and the prospects of him facing Bayern in next Wednesday's quarter-final second-leg appear bleak.
Related ArticlesFerguson fears for United after Bayern blowBayern Munich 2 Man Utd 1Can United win without Rooney?Lyon 3 Bordeaux 1Champions League fixturesUnited horrorshowInitial fears that Rooney had sustaied a World Cup-threatening foot injury he has sustained three previous metatarsal injuries were allayed by United.
But manager Sir Alex Ferguson admits that the club will assess the injury today prior to United's flight back to Manchester.
Ferguson said: 'Wayne has hurt his ankle. It's too early to say the condition of it, but we will know tomorrow (weds). I don't think it is terribly serious, but we'll have to see.
'Will he be fit to play against Chelsea at the weekend? I don't know. I can't answer that. He is certainly being treated by our medics, but we will see what he's like tomorrow.'
To compound matters for Rooney and United, the player was selected by UEFA to undergo a random drug test after the game which prevented the club's medical staff from attending his injury.
By the time he had met the requirements of the drug testers, United's coach had departed for the team hotel, leaving Rooney to return in a waiting car.
With Bayern taking a 2-1 lead to Old Trafford, coach Louis van Gaal admitted that Rooney's likely absence will be a boost for the Germans.
Van Gaal said: 'I don't know if he is injured or how serious it is, but Rooney is very important for United. He is their most important player.
'Look at the statistics. He has 34 goals this season. Then they have 11 own goals as their third top scorer and Berbatov with 12 goals, so that's how important he is to United.'