A 1-0 win for Namibia over the Gambia in Windhoek on Saturday ensured that Burkina Faso cannot be caught at the top of the three-team Group F standings.
However, the Burkinabe face a protest from Namibia that they used an ineligible player in qualifying matches in March and June.
Cameroon-born defender Herve Zengue played in home and away wins over Namibia on the basis of an alleged marriage to a Burkinabe women.
Namibia are arguing he did not fulfil FIFA's criteria to qualify to play for Burkina Faso.
The Confederation of African Football's disciplinary committee will hear the protest in Cairo later this month.
If Namibia win their case they could be awarded six points and after Saturday's win earn an unexpected route to the finals.
Already qualified along with co-hosts Equatorial Guinea and Gabon are Botswana and the Ivory Coast.
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