The Germany international completed pool exercises on Friday but will not be ready for the trip to the BayArena and is a doubt for the return leg in the Spanish capital next week.
Head coach Carlo Ancelotti also confirmed that Boateng is struggling with a muscle complaint and will not be risked this weekend, although he hopes he will be ready to face Madrid.
"Boateng and Hummels will be missing," he told a news conference. "Boateng has adductor problems but he'll hopefully be available against Madrid.
"Without Hummels and Boateng, [David] Alaba will play as a centre-back and [Juan] Bernat on the left. I'll look to see who's a bit tired at training.
"I hope we can take Hummels to Madrid."
Ancelotti, who confirmed that Nicolas Feldhahn will be included in the squad as injury cover, gave a more encouraging update on the fitness of Robert Lewandowski.
The Poland international missed the Madrid defeat but has stepped up his training work in a bid to be 100 per cent fit for Tuesday's game."Lewandowski has trained individually and is feeling good," Ancelotti said of the striker, who is suspended for Saturday's game.