Fati has been out for a month with a hamstring injury and Barcelona have confirmed the 19-year-old has not travelled to Germany.
Martin Braithwaite, Pedri, Sergio Aguero and Sergi Roberto are all still out for new boss Xavi Hernandez, while Ez Abde is unavailable because he is not registered for the Champions League.
Barcelona will secure a place in the last 16 with a win against already-qualified Bayern.
But failure to win will send five-time European champions Barcelona crashing down into the Europa League should Benfica beat Group E bottom club Dynamo Kyiv.
Barcelona will progress to the knockout stage if Benfica do not beat Dynamo Kyiv.
Bayern will be without half a dozen players and coach Julian Nagelsmann is set to field a makeshift side.
Leon Goretzka and Serge Gnabry are nursing minor injures, while Eric Maxim Choupo-Moting is still feeling the effects of a bout of coronavirus. Joshua Kimmich – out for four weeks after being quarantined twice due to Covid – Michael Cuisance and Marcel Sabitzer are not yet fit.
Barcelona starting lineup: Ter Stegen, Alba, Pique, Lenglet, Araujo, Busquets, De Jong, Gavi, Dembele, Depay, Dest
Subs: Puig, Deir, Neto, Coutinho, De Jong, Mingueza, Umtiti, Garcia, Pena, Nico, Balde, Akhomach