Gnabry was replaced by Franck Ribery during the first half of Wednesday's 1-0 success, earned thanks to the substitute's late strike.
Bayern announced Gnabry will be unavailable for Saturday's game against head coach Niko Kovac's former club Eintracht Frankfurt.
But the Bundesliga champions did not offer any potential timescale for the 23-year-old's return to action in a medical update.
"The champions will also have to manage without Renato Sanches," Bayern added in a statement on their official website.
"The Portugal international was shown a second yellow card in the hectic closing stages and now serves a one-match ban.
"In addition to the duo, Bayern are also without the services of Arjen Robben (thigh), James Rodriguez (knee) and World Cup winner Corentin Tolisso (cruciate)."
Gnabry has scored four goals in 14 Bundesliga appearances this season, also contributing two assists in the league.
Kovac's men are third in the table, six points behind leaders Borussia Dortmund, having won four successive league games.
A meeting with Eintracht this weekend will bring their efforts in 2018 to a close, with the German top-flight set to shut down for a winter break following the next round of fixtures.