Neuer had been out of action for several weeks after he underwent knee surgery following Bayern's 3-2 victory over RB Leipzig in the Bundesliga on February 5th.
The 35-year-old returned to the starting line-up on Tuesday, taking back the captain's armband from understudy Thomas Mueller.
The German champions will be hoping their veteran stopper can help rally a defence which has been remarkably wobbly in recent weeks.
French defender Dayot Upamecano, who did not start in the first leg and has faced criticism for his performances in the Bundesliga, was left on the bench once again.
March 8, 2022
Bayern still have several key players out with long-term injuries, including Canadian international Alphonso Davies and Germany midfielder Leon Goretzka.
The six-time winners are out to avoid an upset against Austrian champions Salzburg, who line up with goalscoring prodigy and former Bayern player Karim Adeyemi at the tip of their attack.
Adeyemi started up front alongside Junior Adamu, who scored Salzburg's opener in the 1-1 draw in the first leg.
Starting line-ups:
Bayern Munich (3-2-4-1)
Manuel Neuer (capt); Lucas Hernandez, Niklas Suele, Benjamin Pavard; Jamal Musiala, Joshua Kimmich; Kingsley Coman, Leroy Sane, Thomas Mueller, Serge Gnabry; Robert Lewandowski
Coach: Julian Nagelsmann (GER)
March 8, 2022
Red Bull Salzburg (4-3-1-2)
Philipp Koehn; Rasmus Kristensen, Oumar Solet, Maximilian Woeber, Andreas Ulmer (capt); Nicolas Capaldo, Mohamed Camara, Nicolas Seiwald; Brenden Aaronson; Karim Adeyemi, Junior Adamu
Coach: Matthias Jaissle (GER)
March 8, 2022
Referee: Clement Turpin (FRA)