FIFA have awarded Congo a 3-0 victory after their 0-0 draw in June where Burkina Faso fielded Herve Zengue, a Cameroonian defender who they have controversially continued to use despite repeated questions over his ineligibility.
"The FIFA Disciplinary Committee has decided that the Burkina Faso FA has breached the disciplinary code on ineligibility," read a statement, adding the decision is subject to appeal and is not "final and binding."
"The match Burkina Faso v Congo of 2 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 (£4,050)."
Namibia protested late last year that Burkina Faso's use of Zengue in two 2012 African Nations Cup qualifying matches contravened rules on player eligibility.
They were seeking to be awarded the points from the games, which would have qualified them for the finals instead, but they lost their protest and appeal at the Confederation of African Football and a subsequent bid for redress to the Court of Arbitration for Sport in Switzerland.
Zengue did not qualify to play for Burkina Faso because he was not born in the country, had no blood ties with and had never lived in Burkina Faso, the losing protest said.
Burkina Faso said they had given Zengue a passport because he was married to a Burkinabe woman and then invited him to play for their national team.
FIFA'S decision follows a similar sanction for Gabon, who were found to have used an ineligible Cameroon-born player against Niger in June, and Sudan, who forfeited points for fielding a suspended player against Zambia.
CAF allowed Gabon to use defender Charly Moussono at the last Nations Cup, only for FIFA to find he had previously represented Cameroon in a Beach Soccer World Cup.
African football's controlling body have done little in recent years to deal with countries who import players to strengthen their national teams.
Togo used a spate of Brazilians in recent years while Rwanda, Burundi and Mauritania have also been accused of giving passports to ineligible players so that they can field them in international matches.
The most rampant use of mercenaries has been that of Equatorial Guinea, still to be sanctioned for filling their team with Brazilians, Cameroonians, Nigerians and even a player from the nearby Cape Verde Islands.