Aliou Cisse replaced the first-choice goalkeeper with Alfred Gomis for the tie, where they defeated the Harambee Stars 3-0 to seal a place in the Round of 16 of the tournament.
Mendy, who was in goal for the Teranga Lions’ opening two games against Tanzania and Algeria, has been allowed by the Senegalese Football Federation (FSF) authority to depart for France to undergo surgery to the broken finger.
"After consultation with the authorities, the player Edouard Mendy was allowed to join France for appropriate medical treatment and follow-up," read a statement from the (FSF).
Senegal will take on Uganda in the Round of 16 of the competition at the Cairo International Stadium on Friday.
The Terenga Lions have never won the continental title in their history, with their best performance being the 2002 edition, where they finished as runners-up behind Cameroon.