The Bavarians have won all three of their league matches this year with a 16-3 goal aggregate while protecting an 11-point lead.
They also secured a spot in the Champions League knockout stage a round early with a 2-0 victory over Belgium's Union Saint-Gilloise on Wednesday.
Upamecano has a viral infection that will keep him in bed for several days, and Bayern are already without injured defenders Josip Stanisic and Konrad Laimer as well as Sacha Boey.
"Despite these absences, we still have good competition for the defence," Kompany told a press conference, naming Kim Min-jae, who was sent off in the Champions League on Wednesday and is expected to play on Saturday, Hiroki Ito and Joshua Kimmich, among others.
Bayern are unbeaten in the Bundesliga this season, and cruising towards the title, far ahead of Borussia Dortmund.