Ghana had to settle for a 1-1 draw as Gabon struck two minutes from time through Jim Allevinah to put the Africa Cup of Nations campaign of the four-time champions in peril after a bad-tempered clash on Friday.
Ghana's captain Andre Ayew blasted home a superb left-foot shot for an 18th minute lead but the result leaves them with one point from two Group C matches and in danger of elimination if they do not win their last game against Comoros next Tuesday.
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A testy encounter ended in scuffles and a red card for Ghana's Benjamin Tetteh for his part in the post-match punch up.
Gabon were not allowed to field captain Pierre-Emerick Aubameyang who although out of COVID-19 isolation was not allowed to play by the Confederation of African Football.
"According to the CAF medical commission, the players Pierre-Emerick Aubameyang, Axel Meye and Mario Lemina, barely out of COVID isolation, cannot take part in this match.
"Medical examinations show cardiac lesions and CAF did not want to take any risks," the Gabon Football Federation tweeted.
Ghana, who won the last of their Cup of Nations titles 40 years ago, had lost their opener to Morocco and needed victory to put themselves back in contention for a second round place.
They got off to a vibrant start as Ayew turned his marker and then hit a bullet to break the deadlock after 18 minutes.
But despite facing little threat from Gabon all game, they let it slip as substitute Allevinah caught them cold in the 88th minute with an angled left foot finish.
The match delivered few chances with far too many crunching tackles and the bad blood between the teams continued after the final whistle with an unsavoury punch-up.
The referee brandished a red card afterwards looking to find Tetteh but the player had already fled to the changing rooms after throwing a punch in the fracas.
Morocco had earlier beaten Comoros Islands 2-0 to win the first of the double header at Ahmadou Ahidjo Stadium and they head the group standings with six points.
Gabon are now second on four while Ghana reamin on one and the Comoros have yet to get off the mark.
Gabon are not guaranteed a top-two finish but four points should be enough to ensure they reach the last 16, if not in the top two then as one of the four best third-placed finishers.