The world champions are second in Group H on 15 points, behind Turkey by virtue of their defeat in Konya last June, while Iceland are third with 12 points after six matches.
"After having spoken with the player, who was following a protocol of recovery since Monday, and Franck Le Gall, the doctor of the French team, [manager] Didier Deschamps decided to return the player to his club, Paris Saint-Germain," a statement from the French federation read.
"Kylian Mbappe will leave Clairefontaine Wednesday morning. The staff of the France national team wishes a quick return to Kylian."
Mbappe first suffered the injury back in August on domestic and appeared to re-aggravate the problem after being rushed back to first-team action.