FIFA says it overturned Togo's 2-0 home win against Cameroon on June 9, and awarded the visitors a 3-0 default victory.
Cameroon now rises above Libya in the standings and leads by one point with one match remaining.
Cameroon hosts Libya on Sept. 6 needing just a draw to advance to the final playoff round.
FIFA says Togo played Alexys Romao, a midfielder with Marseille, who should have served a one-match suspension for accumulating yellow cards.
Togo joins Burkina Faso, Equatorial Guinea, Ethiopia, Gabon and Sudan among African teams losing matches by default for administrative errors in the current World Cup qualifying phase.
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