South Africa did not play at the World Cup.
South Africa had appealed against the decision to allow the decisive World Cup qualification match against Ghana to be played.
The only goal in the game was scored from a first-half penalty, and Bafana Bafana claimed they were robbed.
The South Africa Football Association included allegations of match fixing, match manipulation and corruption when it lodged a complaint with football's world governing body.
South Africa needed a draw to get into the World Cup play-offs, but the result meant that they lost out on goals scored.
Danny Jordaan claimed that there was a spike in betting during the match.
An appeal by Benin about the substitution made by DR Congo in a crunch qualifier on the same day has been thrown out.
The decisions are subject to appeal, as the protests did not meet relevant requirements.
The Disciplinary Code and the regulations for the World Cup were referred to by Fifa, but they did not give the reasons for the rulings.
The draw for the African World Cup play-offs will take place in January, with two-legged ties to decide the five teams that will play in the World Cup.
The decision was received without any details and the Safa will request the reasons from the world governing body.
The Leopards qualified ahead of Benin, who had needed a win to advance, because of their 2-0 defeat by DR Congo.
The appeal was about the fact that DR Congo made a total of four substitution during the match.
Under current regulations, teams are only allowed to make up to five replacements during three windows in the game.
