Bayern said their captain suffered a "minor muscle tear" during the 4-1 win over Borussia Monchengladbach in the Bundesliga on Friday.
Runaway leaders Bayern did not give a timeframe on Saturday for his return, but German tabloid Bild reported Neuer will be out for two weeks. That means he would miss both legs against Atalanta as well as the Bundesliga match at Bayer Leverkusen.
Neuer, who turns 40 later this month, has already missed several matches with calf problems this season and was sidelined for 10 games last campaign with a similar injury.
The goalkeeper's deal at the German champions runs until the end of the season. Neuer, who retired from international duty in August 2024, has yet to indicate whether he will try to stay on for another year.