Mali had taken an early lead after striker Bakary Sako, who plays for Wolverhampton Wanderers in the English Championship, superbly powered home a right foot volley from close range.
The goal looked to have been enough for Mali, who defended stoutly against an Ivory Coast team featuring the likes of Manchester City's Yaya Toure and Wilfried Bony.
But The Elephants pushed hard for an equalizer. Winger Max-Alain Gradel clinched it, scoring with seven minutes remaining. The Ivory Coast are now top of the group on two points with one game to play.
Despite the late goal, Ivory Coast's French coach Herve Renard, a previous winner of the tournament as coach of Zambia, was not happy with some of the officiating, especially a first half penalty appeal for a foul on Wilfried Bony.
"I won't talk about anything but I was not upset against my players. I think you are able to understand against what I was upset, but now it is too late to talk about that," Renard cryptically told AFP.
"I don't like to create controversy after. All that leads to is being suspended. I need to remain calm," he added.
"There were lots more good things today than in the first match but unfortunately we went behind early on. Once again we struggled at the start of the game. I think if you look at the statistics, they didn't have many shots on goal."
Group D's other two teams, Cameroon and Guinea, played out an entertaining 1-1 draw.
Cameroon took the lead rather fortuitously when a Benjamin Moukandjo corner went straight in before a goal by the highly rate Ibrahima Traore before half time leveled the match.
The group is now delicately poised going into the final round of games, with all four teams on two points after four consecutive 1-1 draws.