The Bavarian giants travel to Glasgow this week sitting second in Group B, three points below leaders Pairs Saint-Germain and three points above their upcoming opponents.
However, Bayern have opted against including Lewandowski in their squad after the striker suffered a a thigh injury in this past weekend’s Bundesliga win over RB Leipzig.
Bayern chief executive Karl-Heinz Rummenigge said: "If we had played against Real Madrid, he might have gone.
"The coach does not want to risk anything as Saturday's game, which is very important for us, is in the back of his mind."