The visitors from the Democratic Republic of Congo appeared to be cruising to victory after 51 minutes when Daniel Agyei doubled their advantage following Cheibane Traore's first-half opener – Rainford Kalaba the provider on both occasions.
But Kone gave Malien a foothold in the game in the 74th minute and he struck again two minutes later to reignite the Malian outfit's hopes of reaching the group stages.
In Saturday's other tie, Al Merreikh of Sudan claimed a shock 1-0 win at home to ES Tunis.
Alaeddin Youssef netted decisively from the penalty spot after 24 minutes before goalkeeper Sami Helal starred with a succession of fine saves to keep the Tunisian champions in the tie ahead of the second leg.
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