Arturo Vidal had given an early lead to Bayern by netting in the 25th minute.
After being sent off in the first leg, Javi Martinez is suspended, while Jerome Boateng is out with an adductor problem.
Of Ronaldo's haul in Europe's top competition, he has managed 82 for Real, with the other 16 coming for Manchester United, and his double took him four goals ahead of Lionel Messi (94) in the race to become the first player to score 100 Champions League goals.
After a hard loss, Bayern manager Carlo Ancelotti was quoted to be saying by Reuters, "Small details have decided the game".
Lewandowski, 28, was expected to lead Carlo Ancelotti's side on Wednesday night following another productive campaign, in which he has scored 38 goals in 40 appearances. You have to tell me who doubts me because none of it has come to me.
The Frenchman said: "Winning here isn't easy".
"We played a very good first half".
The second half would belong to Spanish titans. "At the break we were happy to only be 1-0 down".
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I haven't been so excited and yet so perplexed about a movie since, well, the Beauty and the Beast remake was announced. The day was celebrated in an organized manner for the first time in 2011 at the Toronto Underground Cinema.
'Gareth is not going to be with us against Sporting, that is clear, ' Zidane said at his pre-match media conference.
The French global then converted from the spot to give Atletico a slender advantage going into the return leg at the King Power Stadium on Tuesday.
Ronaldo remains two short of reaching a ton of Champions League goals, having scored once in a qualifier and twice in the UEFA Super Cup. That is his ambition. We showed patience and we showed the willingness to get the right result. We are taking it game by game.
"We know Cristiano's position on the field, but he had the freedom during the game to go wherever the ball fell".
"We suffered here but all-in-all it's not easy to play here".
But Ronaldo - who admitted on Wednesday that he has altered his training programme to reduce the risk of injury - is confident that the entire squad is ready for the run-in.
"When I started scoring goals in the Champions League, I never imagined I'd beat this record. We are hoping to reach the semi-finals". "I'm happy with the substation because Marco did well out there".
The second leg of Madrid's Champions League quarter-final tie against Bayern Munich takes place just three days later, before Barcelona visit Santiago Bernabeu for El Clasico next Sunday.
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