After the lights had literally gone out on the match, the start was delayed some 12 minutes and it was Mali who seemed to settle first, winning a succession of corners.
Bassala Toure had the first real opening on 22 minutes, however he scuffed his shot and the danger was cleared.
The longer the half wore on, the more comfortable Benin looked as they reduced the Mali players to shooting from distance, with no success.
A 0-0 scoreline at the break would have delighted the Benin faithful, who were hopeful their side could nick a goal on the break, especially with the pacy Helsingborgs striker Razak Omotoyossi up front.
But disaster struck just after halftime as Kanoute’s shot was only parried out by Benin keeper Rachad Chitou, and as Dramane Traore went to latch onto the rebound, he received a shove in the back from 38-year-old veteran defender Alain Gaspoz and South African referee Jerome Damon had no hesitation in pointing to the spot.
Kanoute duly converted to open his account for the tournament, and from there on in Mali seemed content to absorb the Benin pressure.
And they did so well until the final 10 minutes when goalkeeper Mahamadou Sidibe was forced into a number of top-class saves, and the Mali defence scrambling to clear to their lines.
But they managed to hold onto the win and join the Ivory Coast on three points after their 1-0 success over Nigeria in the day’s earlier game in Sekondi.
Mali 1 (Kanoute 49pen)Benin 0
Yellow cards: Mahamadou Diarra, Bassala Toure, Adama Coulibaly; Abdul Adenon, Alain Gaspoz
Mali: 1 Mahamadou Sidibe, 22 Oumar Sissoko, 4 Adama Coulibaly, 15 Cedric Kante, 5 Souleymane Diamoutene, 18 Souleymane Dembele, 12 Seydou Keita, 6 Mahamadou Diarra, 8 Bassala Toure (Drissa Diakite 72), 10 Dramane Traore (Mamadi Sidibe 55) (Samy Traore 89), 19 Frederic Kanoute
Benin: 1 Rachad Chitou, 3 Abdul Adenon, 14 Alain Gaspoz, 5 Damien Chrystosome, 15 Anicet Adjamossi, 6 Jonas Oketola (Stephane Sessegnon 53), 7 Romauld Boco, 18 Seidath Tchomogo, 19 Jocelyn Ahoueya (Wassiou Oladipikpo 84), 8 Razak Omotoyossi, 10 Oumar Tchomogo (Abou Maiga 70)