Gabon forfeited by a mandatory 3-0 scoreline a match against Ivory Coast in Libreville for fielding suspended midfielder Merlin Tandjigora.
However, the Gabonese lost the match 3-0 so the punishment effectively amounted to a $6,200 (5,300 euros) fine.
Fielding ineligible players was a major problem in Africa during 2014 World Cup qualifying, but Portugal-based Tandjigora is the first culprit since.
Nigeria were fined $30,000 after spectators invaded the pitch in Uyo during a 4-0 triumph over Cameroon.
The Democratic Republic of Congo must pay FIFA $20,000 after the crowd hurled bottles and let off incendiary devices during a 2-2 draw with Tunisia in Kinshasa.
Mali were fined $15,000 because fans flung bottles and chairs on the pitch in a 0-0 stalemate with Morocco in Bamako.
The earlier qualifier between the same countries in Rabat led to a $3,000 fine for Morocco over whistling while the Malian national anthem was being played.
Zambia received a $7,000 fine after the crowd hurled various unspecified objects on the pitch during a 3-1 victory over Algeria in Lusaka.
Senegal and Burkina Faso were warned for late kick-offs in the qualifiers between them in Dakar and Ouagadougou.
The fines are a serious blow as most African national football associations struggle financially with many relying on government bailouts for survival.
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