The Morocco international was replaced by Jerome Boateng late in the first half of the 2-0 Bundesliga victory over Mainz at the Allianz Arena.
Bayern's official Twitter account confirmed Benatia will miss the clash with Mainz.
The Bavarian club will also assess the fitness of striker Robert Lewandowski and midfielder Xabi Alonso after they were also withdrawn during Tuesday's victory.
Lewandowski came off at half-time following a strong challenge and Alonso's game was cut short at the hour-mark, so they will be monitored ahead of the Bundesliga champions' final match before the winter break.
Arjen Robben and Thomas Muller were on target as Bayern stretched their unbeaten run to 20 Bundesliga game to go eight points clear of second-placed Wolfsburg.
Coach Pep Guardiola believes the Bundesliga champions should have won by a more emphatic margin and criticised Freiburg's negative approach.
He said: "I'm very pleased. Freiburg did very well defensively today but we were excellent in attack.
"We had 13 clear-cut chances and their keeper made some very good saves.
"Great credit to my players and now we need to take the final step in Mainz."
