The Uruguayan is still in quarantine after a positive coronavirus test which saw him miss the game against his former club, Barcelona, last week, as well as the weekend win away at Valencia.
A negative test will need to be recorded before he can return, with the same being said for Lucas Torreira.
Diego Costa and Sime Vrsaljko will also not feature due to injury, while there are doubts over the availability of Hector Herrera due to a muscular problem.
The Mexican is, however, back in training.
Against Valencia at the weekend, Diego Simeone actually changed from his usual 4-4-2 to a 3-4-2-1 formation. But, it is likely he will revert back to his usual set-up for the Bayern game.
For Bayern, they will again be without Joshua Kimmich and Alphonso Davies who are both on the long-term injury list.
Leroy Sane came off the bench against Stuttgart, having once again been left out of the starting XI. When Hansi Flick was asked why the summer signing from Man Ciity was not starting more games, he said:
“He is still 100 per cent fit.
“His efficiency is great. But like other players, he unnecessarily lost the ball a couple of times against Salzburg and in some instances, he didn't quite pursue one-on-ones. There are reasons for it, and we talked about that. He will try to do better next time.
“When he comes on the pitch, he creates a certain dynamic in the team, increases it. In the last couple of games, he has always scored after being subbed in. That's what makes him stand out and he has quality.
“It is obvious that he still needs time after a long injury, and he will get that time. He works hard in training.
“We are pleased with him, but it is important that when he starts a game, he gives a 100 per cent. We are working on that.”
Judging by Flick's words, Sane might not start this one due to the level of opponent.
Bayern will be without Marc Roca after he was sent off against RB Salzburg in the previous Champions League clash.