The Pole, who with seven goals is joint third top-scorer in the Champions League this season, together with Borussia Dortmund's Pierre-Emerick Aubameyang, has not recovered from the right shoulder injury he sustained in Saturday's Der Klassiker win over Dortmund.
Watch: Bayern 4-1 Dortmund - highlights
The 28-year-old was unable to train more than 20 minutes on Tuesday and Bayern coach Carlo Ancelotti said he would decide on his involvement after a fitness test on Wednesday. That was performed prior to Bayern's departure for the Allianz Arena, and the result was negative with the Pole left out of the matchday squad.
Thomas Müller will take his place and lead the Bayern line, with Ancelotti confident the Germany international will deliver the goods. "Whether Lewandowski plays or not won't affect our strategy or our confidence for the game," he said pre-match.