Herve Renard's side only earned a 1-1 draw with Guinea in their opening match courtesy of Seydou Doumbia's 72nd-minute strike, and looked set to suffer a huge setback on Saturday as, despite dominating possession, they struggled to find a response to Bakary Sako's early opener.
However, substitute Max Gradel fired home with three minutes remaining following a cutback from Serge Aurier, providing a welcome boost to the Ivory Coast's qualification hopes.
Sako fired Mali ahead after just seven minutes with a superb half-volley, although the Ivory Coast - many people's tip to win the tournament - appeared unfortunate not to be awarded a penalty prior to the interval when Molla Wague upended Wilfried Bony in the area.
Mali, who lost goalkeeper Soumbeila Diakite to injury in the second half, held out thereafter against wave after wave of pressure, only to be found wanting as Gradel finally broke their resistance.
Both teams will enter the final round of group matches with two points from as many games.
Siaka Tiene, Ismael Diomande and Doumbia were all brought into an Ivory Coast side missing the suspended Gervinho.
Yet it was an unchanged Mali who seized the initiative early on, courtesy of a fine goal from Sako.
Sambou Yatabare was given time to deliver a cross from the right, which Sako met with a sweetly timed half-volley back across goal that left Sylvain Gbohouo with no chance.
A lack of quality in the final third hampered the Ivory Coast as they sought to get back on level terms, with Aurier particularly wasteful as he failed to pick out a team-mate after getting to the byline.
However, Mali appeared extremely fortunate not to concede a penalty in the 33rd minute when Wague brought down Bony with his head as he fell to the ground, after the striker had pulled off a nutmeg with a dazzling piece of footwork.
Kolo Toure saw a powerful header superbly parried on to the crossbar by Diakite from the corner that followed as Mali continued to ride their luck, while Doumbia volleyed wide after being incorrectly flagged offside.
Diomande was then hauled off six minutes before the interval, replaced by Gradel, but the change did little to bring about an immediate improvement for the Ivory Coast.
As Mali dropped increasingly deep in the second half, Bony twice missed the target with headers.
The injured Diakite was then forced off with an apparent thigh injury, yet Mali continued to hold firm and could have snatched a second when Gbohouo made a mess of a cross only to be rescued by Wilfried Kanon's clearance.
Just when it seemed as though Mali had done enough to secure three points, Gradel had the final say, firing home a low shot following fine work from Yaya Toure and Aurier.
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