Mustafi tore a hamstring muscle in the match against Algeria and has been ruled out of the remainder of the tournament. He will remain with the team.
Assistant coach Andreas Kopke said backup midfielder Christoph Kramer had a light fever on Wednesday but was expected to be available.
Central defender Mats Hummels has recovered from the flu, which forced him to miss the 2-1 extra-time victory over Algeria on Monday.
Midfielder Bastian Schweinsteiger had cramps and had to be substituted late in that game but Koepke said he has recovered.
Germany will beat France, Elephant predicts
Elephant oracle "Nelly" predicts Germany will beat France in the World Cup quarter-final.
Mustafi out of World Cup
Germany's Shkodran Mustafi was ruled out of the World Cup after suffering an injury and will play no further part in Germany's campaign.
Deschamps prepares squad for Germany
French manager Didier Deschamps told the media he would not discuss the 1982 and 1986 World Cup defeats against Germany.
A true heavyweight battle
The Germans must improve in the attacking third if they are to advance to the World Cup semifinals. Joachim Low's squad has been left vulnerable on the counterattack, while France may be one of the best teams left in Brazil from the midfield.