Bayern issued a statement saying the two were "closing in on a comeback" after returning to individual training.
Musiala missed Germany's Nations League wins against Bosnia and the Netherlands along with a 3-3 draw at Eintracht Frankfurt with a hip issue, while Upamecano was ruled out for France's away wins over Israel and Belgium with a muscle injury.
Forward Harry Kane, who missed England's loss to Greece at Wembley, returned to full team training with Bayern on Tuesday.
Bayern sit atop the Bundesliga table, ahead of RB Leipzig on goal difference, after six games before Saturday's home clash with Stuttgart.
The German giants are winless in three matches after successive Bundesliga draws against Bayer Leverkusen and Eintracht Frankfurt along with a 1-0 Champions League loss at Aston Villa.