Sevilla forward Frederic Kanoute was also hurt as angered Togo supporters attacked their opposite fans as well as Mali players.
Goals from Kanoute and Mamadou Diallo had sealed the win.
"Mamady Sidibe took a blow, doubtless with a weapon, which caused bruising to his arm," Mali coach Jean-Francois Jodar told L'Equipe.
"Frederic Kanoute was hit with a belt. It was like a battlefield, there was blood everywhere in the dressing room."