The Football Association of Zambia protested after they felt that referee Joshua Bondo was not fair in his handling of the match.
Nigeria clinched a 1-0 win and qualified for their third straight World Cup with a match to spare in Group B.
As a result, FAZ were aggrieved and filed a formal protest to FIFA asking them to look into the matter after their goal was disallowed by Bondo.
The goal in question was scored after one of the assistant referees had clearly flagged for an offside and effectively stopped play.
However, in a letter addressed to FAZ and signed by Julien Deux of the FIFA Disciplinary Committee, the world football governing body dismissed the case for lacking merit.
Deux told the Zambians to accept the result and referring them to Article 15, Paragraph 6 of the World Cup regulations.
FIFA said there was “no evidence of any infringement of the regulations by the referees”.