The powerfully-built Queens Park Rangers player is joined on the sidelines by goalkeeper Mamadou Samassa, who was also in the squad at the recent African Nations Cup in which Mali finished third.
AC Milan's Bakary Traore and uncapped Abdoulwhaid Sissoko of Brest in Ligue 1 have also withdrawn. Traore was recalled to the squad after missing the tournament in South Africa.
Sissoko, younger brother of midfielder Momo Sissoko, had ben called up for the first time.
Mali have three points from their first two matches in Group H. Hosts Rwanda have a single point.