كتب : Hatem Maher
The victory put Mali level with Ivory Coast on three points after the Elephants edged past Nigeria 1-0 earlier in the day.
Sevilla playmaker Seydou Keita was the architect of Mali's attacking attempts during the first-half.
In the 12th minute, Kanoute's shot was blocked by a defender and the ball slipped to Keita, whose powerful drive went just wide.
Benin responded one minute later when a mis-timed jump by Mali keeper Mahamadou Sidibe allowed Oumar Tchomogo to rise unmarked at the far post but his free header missed the target.
Mali were awarded a deserved penalty two minutes after the interval.
Kanoute's shot was parried by Benin keeper into the path of Dramane Traore, who went down under a challenge from Alain Gaspoz while attempting to poke home.
Sevilla top scorer Kanoute stepped-up and sent the keeper the wrong way to break Benin's resistance.
Benin could have secured a valuable equalizer seven minutes from time but Sidibe was on alert to block two successive shots from Stephane Sessegnon and Abou Maiga.