There were question marks over two of Real Madrid's goals as Ronaldo appeared to be in offside positions, but the 32-year-old saw his side as "fair winners" on the night.
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.
Real Madrid hosted Bayern Munich at the Bernabeu tonight, and came into the game holding a 2-1 advantage from the first leg. We played with one less man at home and here, too.
Marcelo twice cleared off the line for Madrid and Jerome Boateng did the same for Bayern in a thrilling game, which was tilted in Madrid's favour by Arturo Vidal's dismissal for two yellow cards, the second of which was harsh. He scored 3 goals.
Zidane said: "In the key moments Ronaldo is always there".
The talisman's hat-trick meant he became the first player to score 100 Champions League goals. "I think the team deserved to go through". It was Ronaldo's sixth Champions League treble, one behind Barcelona forward Lionel Messi who has tallied 94 goals in the competition.
Robert Lewandowski gave the Bundesliga champions the lead from the penalty spot, after Arjen Robben was fouled in the area.
Cristiano Ronaldo scored a hat-trick as the holders won 4-2 but the German team had every right to be annoyed after Arturo Vidal's sending off in the 84th minute.
Marco Asensio then grabbed a fourth on the night for Madrid as 10-man Bayern began to wilt and their European dream died. In trying to snuff out Lewandowski after substitute Thomas Müller had helped the ball along, the ball bounced off the Real Madrid captain and creeped into his own net.