His goal shortly after halftime ensured a win for the first time in more than 40 years at the finals for Congo, who are now on four points.
Burkina Faso played out a goalless draw with hosts Equatorial Guinea in the earlier match at the Estadio de Bata.
It means Gabon are now second in the standings with three points, Equatorial Guinea have two and the previously fancied Burkinabe one.
It sets up the potential of a thrilling finish, and the possibility of a three-way tie at the top of the standings, when the group is concluded on Sunday.
Congo’s goal came in the 48th minute as Gabon failed to clear a corner with a weak header falling to Oniangue, who hooked the ball towards goal. It looped over the top of the defence and went in with goalkeeper Didier Ovono rooted to the spot.
Gabon dominated an exciting game but ran into a Congo side full of determination and spirit. It was their first win at the finals since 1974.
“We did not play up to the standards we could have, they didn’t give us any chance to get any rhythm,” said Gabon skipper Pierre-Emerick Aubameyang.
Playing in front of another sizeable partisan crowd, Equatorial Guinea earlier had to rely on the counter attack as Burkina Faso failed to convert the game's best chances, hitting the woodwork twice.
Burkina Faso went close in the 20th minute when Alain Traore's whipped 30-metre free kick smashed Felipe Ovono's right post.
The competition hosts were again saved by the woodwork in the 39th minute when Ovono deflected Traore's volley from close range onto his post.
The Equatorial Guinea keeper was involved again five minutes from the interval, parrying away Bertrand Traore's powerful long-range effort.
Equatorial Guinea, however, looked dangerous on the break.Shortly after the hour, Kike's fierce shot was blocked by Burkina keeper Moussa Germain Sanou in their best chance of the game.
(Additional reporting by Julien Pretot and Nick Said; Editing by Justin Palmer)
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