The Polish striker was left out of the squad by manager Carlo Ancelotti ahead of the match at the Allianz Arena, which kicks off at 7.45pm.
Lewandowski scored twice against Borussia Dortmund on Saturday to take his season’s goal tally to 38 in 40 matches. However, he was taken off after 72 minutes with a shoulder problem.
Ancelotti said on Tuesday that the 28-year-old’s participation depended on how the striker felt.
"Robert Lewandowski trained today, just 20 minutes because he had a problem in the last game," Ancelotti said.
"This morning he had a good sensation. We will check definitely tomorrow. If he doesn't have pain he is going to play; if he does have pain he will not play."
Lewandowski, who will be replaced by Thomas Muller in the striker's role, should be fit for the return leg on Tuesday, April 18 in Madrid, while goalkeeper Manuel Neuer is fit again after missing the past three Bundesliga matches with a foot problem. Centre-back Mats Hummels is out with an ankle injury.
Read the full article on eurosport.co.uk: Bayern's Lewandowski out of Real Madrid quarter-final clash with shoulder injury