The German superstar tested positive for coronavirus 11 days ago and needs to return a negative test at least 48 hours before the Lazio game, which has not happened so far, meaning he will not play.
Joining Muller on the Covid-19 positive list is Benjamin Pavard, who is also in self-isolation, having missed the weekend defeat against Eintracht Frankfurt.
In that game, Niklas Sule was asked to play right-back and Hansi Flick will probably do so again rather than ask Bouna Sarr to step in.
The back four will therefore probably be made up of Sule, Jerome Boateng, David Alaba, and Alphonso Davies.
Bayern also have a number of non-Covid related absences as Serge Gnabry, Douglas Costa, Corentin Tolisso, and Tanguy Nianzou are all set to miss out.
Gnabry has a thigh injury and although there is a very small chance he could feature, it is not looking likely.
Marc Roca started against Frankfurt at the weekend but with Leon Goretzka returning from the bench, he will likely drop out of the starting XI for the German, who will partner Joshua Kimmich.
Eric Maxim Choupo-Moting played there against Frankfurt to little success, which could mean 17-year-old Jamal Musiala being thrown in from the start.
Lazio have injury concerns of their own, with Luiz Felipe, Stefan Radu, Thomas Strakosha, Silvio Proto all missing.
Simone Inzaghi fielded a 3-5-2 formation against Sampdoria at the weekend, and will probably do so again in an attempt to pack the midfield against the defending Champions League winners.
None of the injury worries for Inzaghi are fresh, so he could opt to field the same XI that won 1-0 versus Sampdoria.
Ciro Immobile will obviously start up top, and has been partnered recently by Joaquin Correa who has been moved into a more central role having previously been deployed on the wing for the Biancocelesti.