"Serge and Manu won't be available," Kompany told reporters, citing "rib pain" as the reason for Manu's absence.
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The 38-year-old goalkeeper failed to take part in training on Friday, and Kompany did not indicate when he would return.
Neuer and Gnabry join Bayern's long injury list, which includes England captain Harry Kane, Joao Palhinha, Josip Stanisic and Hiroki Ito.
Neuer picked up the first red card of his 866-game career in Tuesday's German Cup loss to Bayer Leverkusen after a first-half collision with Jeremie Frimpong.
Israel goalkeeper Daniel Peretz replaced Neuer in the 17th minute, making his Bayern debut.
With usual back-up goalie Sven Ulreich still missing due to personal leave, Kompany confirmed Peretz would take the field on Saturday.
Kane injured his hamstring in Saturday's 1-1 draw at Borussia Dortmund and missed the loss to Leverkusen, but returned to individual training on Thursday.
"It looks good," Kompany said of Kane's recovery. "The way it's going now, it looks like he could play one or two games in the calendar year, if everything goes well."
Before going down with injury, Kane scored 20 goals in 19 games in all competitions for Bayern this season.
Despite Tuesday's German Cup elimination, Bayern are unbeaten in the league and are currently four points clear of second-placed Eintracht Frankfurt at the top of the Bundesliga table.
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