While Kompany will remain in hospital for a few more days after his collapse on Thursday and will be unavailable to the German record champions for weeks, Joshua Kimmich, Luis Diaz, Jamal Musiala and Min-Jae Kim are also missing from the squad in the Breisgau. Deputy Aaron Danks still has plenty of quality to call on, despite a depleted squad.
At Saturday's press conference, Danks confirmed Kim's absence while standing in for Kompany. Kim suffered a "muscle strain" in Wednesday's Champions League match against Arsenal and had to go off at half-time. Dayot Upamecano and Jonathan Tah are therefore likely to form the centre-back pairing.
Kimmich also remains absent following the death of his father. "He is still with his family and is going through a difficult time at the moment. He will be given all the time he needs," Danks said. Aleksandar Pavlovic and Tom Bischof could again play in central midfield, as they did against the Gunners.
Diaz came on against Arsenal but was then substituted, and is dealing with a muscle bundle tear. He is likely to be out for four to six weeks. Jamal Musiala remains in recovery training after his muscle fibre tear, but could return by the end of October.
Who will be fit for the Borussia Dortmund match? Bayern Munich sweat on several players
In attack, hopes rest on Harry Kane, Michael Olise, Serge Gnabry, Ismael Saibari and Lennart Karl. Left-back Nathaniel Brown could also fill in, as he did at the start of the season.
After the Freiburg match, Bayern Munich continue their DFB Cup campaign in midweek, with 1. FC Magdeburg hosting the defending champions on Wednesday. A major clash with Borussia Dortmund follows the next Saturday.