However, Madrid regained momentum after Arturo Vidal was shown his second yellow card.
Bayern Munich were eliminated from the quarter-final stage after a 4-2 defeat to Real Madrid on the night, that made it 6-3 on aggregate.
Bayern CEO Karl-Heinz Rummenigge said after the match that Neuer sustained the injury as Real scored one of Cristiano Ronaldo's goals which fired them into the semifinals, and suggested that the goalkeeper would miss the rest of the domestic season and also the build-up to the Confederations Cup, which begins in Russian Federation on June 17.
And Vidal was less than impressed with Kassai's performance at the Santiago Bernabeu.
"I'll stick with the good things, the team were very good, we played very well".
Cristiano Ronaldo scored a hat-trick, including two crucial strikes that were offside, as 10-man Bayern rued their luck at the Estadio Bernabeu.
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"We are not happy about this". "They are trying, but it is the moment to bring in video referees".
Madrid were once again grateful to Ronaldo's killer touch as the four-time World Player of the Year was pivotal in both legs against Bayern. Arjen Robben lashed the rebound into the side-netting.
Jerome Boateng bailed out a rare mistake from goalkeeper Manuel Neuer as he cleared off the line from Ramos after Neuer fumbled a simple cross.
Lewandowski appeared to be fractionally offside in the buildup to Sergio Ramos's own goal, causing panic in the area before the defender prodded the ball past Keylor Navas. Worse was to follow for Bayern when, as the first half of extra time was drawing to a close, Ronaldo scored from an offside position and seemingly helped the ball down with his upper arm. In the key games, he's always there.
"I understand the public and Cris", he said.
"The decisions penalised us a lot".