FIFA dismissed South Africa's protest following the 1-0 loss to Ghana in their decisive World Cup qualifier in Cape Coast last month, with the country's football association [SAFA] saying they will consider further steps once they read the judgement.
FIFA's Disciplinary Committee decided that the protest was inadmissible, without providing any further details.
SAFA believe they were "robbed" by Senegal referee Maguette Ndiaye and his assistants, who handed the home side a dubious penalty and made several other doubtful calls.
The result allowed Ghana to leapfrog South Africa to the top of their pool and move into the final stage of qualifying in March for the finals in Qatar next year.
"We have received the decision without details and will request the reasons [from FIFA] and consider our options," SAFA chief executive Tebogo Motlanthe said in a statement on Friday.
South Africa had been hoping to benefit from the precedent set when they were ordered to replay their World Cup qualifier victory over Senegal five years ago, after Ghanaian referee Joseph Lamptey was found guilty by FIFA of unlawfully influencing the result.
Lamptey was banned for life while Senegal won the replay 2-0 and qualified for Russia 2018.