The last qualifying match which ended in a 1-1 draw in Algeria has been overturned by FIFA and Algeria awardeda 3-0 win.
The Nigeria Football Federation has also been fined US$6,000 for the oversight.
Nigeria still maintain their World Cup qualification as they had won a place in Russia before the Algeria game.
Nigeria fielded Abdullahi Shehu against Algeria even thought that the player had two yellow cards from their two previous matches.
The defender was cautioned in the Super Eagles 1-0 win over Zambia in October that sealed Nigeria’s spot in Russia, having been shown a yellow card in the first leg of their second round tie against Swaziland in November 2015.
It means that Nigeria still finish top of Group B but with 13 points instead of 14 while Algeria’s total at the bottom is now four rather than 2 points.