Victory left Congo top on four points from two games, one more than Gabon and two ahead of hosts Equatorial Guinea, who were held to a 0-0 draw by Burkina Faso (one point) in the afternoon fixture.
Captain Prince Oniangue scored an opportunist 48th minute winner to put the Congolese within touching distance of the knockout stages, a scenario which looked improbable after they were beaten by Rwanda over two legs in the preliminary qualifying rounds.
Congo were reinstated into the competition after their opponents were found to have included an ineligible player.
(Writing by Zoran Milosavljevic; editing by Justin Palmer)
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