The African nation have been docked points and fined by the governing body after they repeatedly fielded an ineligible player in competitive international matches
Cameroon-born defender Herve Xavier Zengue has not been cleared to play for les Etalons, but was used in a number of competitive games, prompting the football authorities to take action.
"The Fifa Disciplinary Committee has decided that the Burkina Faso FA has breached the disciplinary code on ineligibility," an official statement by Fifa reads.
"The match between Burkina Faso and Congo on the 2nd of June 2012 is declared to be lost by forfeit [0-3] by Burkina Faso, and the Burkina Faso FA have been fined 6,000 Swiss francs [€4,950]."
Despite his ineligibility, Zengue has been capped six times for Burkina Faso and was given a passport after marring a local woman.
He was called up to the team despite the fact that he has no blood ties or has ever lived in the country, which prompted Namibia to call Fifa to investigate, but their initial accusations were refuted.
Incidents of similar nature are not uncommon in African football as both Gabon and Sudan have been punished in the past for breaching of the same rule.