The People's Elephant lost their last group stage encounter 0-2 away to of the Ivory Coast and needed at least a point to be in contention to qualify from the group stage.
The game away to Djoliba was a tough encounter which ended goalless after the first half with the Nigerian side soaking up the pressure away from home.
Djoliba also needed three points in their home fixture as they will be travelling away to Williamsville for their last group encounter.
With just a minute left of the regular 90, Enyimba however found their breakthrough in the encounter.
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Farouk Mohammed converted a late penalty awarded by the referee in the 91st minute of the encounter.
Enyimba held on for the remaining minutes in extra time awarded to leave the Complex Sportif Hérémakono in Bamako with all three points.
The result means that Enyimba are second in the group with nine points, Cara Brazzaville of Congo also have nine points but are on top with a better goal ratio, Willamsville of Ivory Coast can still qualify as they are third with seven points, while Malian side Djoliba have just four points.
Enyimba will have to finish in the top two in their group to progress to the next round of the competition with just two group games left to play
The People's Elephant have a chance to seal qualification to the next round at home against Cara Brazzaville on Wednesday, August 29, Enyimba lost the first leg away 3-0.