The Germany international goalkeeper sustained the injury as Cristiano Ronaldo completed his hat-trick in extra time during the 4-2 defeat to Madrid in the return leg of their quarter-final tie, which eliminated Bayern 6-3 on aggregate.

Bayern announced the initial diagnosis and said 31 year-old Neuer will "undergo a thorough examination on arrival in Munich prior to a decision on the appropriate treatment".

Neuer had only recently returned from foot surgery against Madrid in the first leg, having missed two Bundesliga fixtures after a training incident last month.

News of Neuer's injury capped a forgettable trip to the Spanish capital for the Bundesliga champion.

Carlo Ancelotti and his men were left raging after midfielder Arturo Vidal was controversially shown a second yellow card with six minutes of normal time remaining.

Also, two of Ronaldo's goals appeared to be offside in extra time at the Santiago Bernabeu.

Bayern - eight points clear in the Bundesliga - is back in action on Sunday (AEST), hosting relegation-threatened Mainz.