Germany goalkeeper Manuel Neuer will not feature again for Bayern Munich this season due to a broken metatarsal, the Bundesliga champion has confirmed.

The 31-year-old 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 UEFA Champions League quarter-final tie, which Bayern lost 6-3 on aggregate.

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.

"I am sad that I will not be available to the team for the season finale," Neuer told Bayern's official website.

"Now I am concentrating on getting back to full health as soon as possible."

Bayern is eight points clear at the top of the Bundesliga with five game remaining, the next of which comes on Sunday (AEST), when relegation-threatened Mainz visits Allianz Arena.