The Tottenham striker "suffered an injury to his lower jaw on Saturday against Manchester United," the FFF said.
Kolo Muani was replaced at half-time as Tottenham drew with United in the Premier League.
After the game, Tottenham manager Thomas Frank did not specify the 26-year-old Frenchman's injury, saying only that it was "nothing big".
Kolo Muani was the second highest international scorer in the squad with nine France goals behind Kylian Mbappe who has 53.
Kolo Muani became the latest attacking casualty for France coach Didier Deschamps.
Paris Saint-Germain duo Ousmane Dembele and Desire Doue are injured. Marcus Thuram is just returning to competition with Inter Milan after more than a month out with a thigh injury and has not been called up.
The 32-year-old Thauvin of Lens, a World Cup winner, returned to the squad in October six years after his last appearance and scored his second international goal in a 3-0 win over Azerbaijan.
Victory over Ukraine on November 13 at the Parc des Princes would ensure France's qualification for the tournament in North America.
If they fail, Les Bleus will have another opportunity against Azerbaijan in Baku on November 16.