The People's Elephant picked up a vital three points in against in their last group encounter to put themselves in a favourable position to advance to the next round.
Enyimba needed at least a point to progress to the quarter-finals but three to be sure depending on the result in the other group game between Williamsville of Ivory Coast and Djoliba.
The first half ended goalless as the Congolese side maintained their spot on the top of the group frustrating the efforts of Enyimba who were playing in their home turf for the first time in three years.
The Ivory Coast side knew that a draw away from home will secure their qualification regardless of result elsewhere and continued to deny the Enyimba.
The Peoples Elephant lost the first leg away 3-0 away from home and were also wary of the threat posed by their West African rivals.
The second half was lively for the homes side but were unable to convert any of their chances.
The game ended in a 1-0 win for Enyimba through a late goal by Wasiu Alalade in additional time.
The result of the game means that Enyimba finished as group winners with 12 points from six games while despite the defeat to CARA Brazzaville they progressed to the next round as runners-up with 10 points as Williamsville were held to a goalless draw in the other group fixture.
Both teams await the winners from the last group which will determine their opponents in the next round, with USM Alger, Rayon Sport and Gor Mahia all with a chance to qualify.