The South African Football Association wants to challenge the decision by FIFA to order a replay of the 2018 FIFA World Cup qualifier between South Africa and Senegal.
The result of the match played in November last year in Polokwane which South Africa won 2-1, has been nullified.
According to FIFA, this decision follows the confirmation of the Court of Arbitration for Sport (CAS) to uphold the lifetime ban of Ghanaian match referee Joseph Lamptey for match manipulation.
SAFA says Bafana Bafana cannot be punished for something they did not do.
The initial ban on the match official by FIFA was upheld by the CAS.
Lamptey awarded South Africa a controversial penalty, that saw the home side score through captain Thulani Hlatshwayo.
According to the letter from FIFA, the match will be replayed within the November 2017 international window, with the exact date to be confirmed in due course.
SAFA president, Danny Jordaan says "FIFA has made it clear that this has nothing to do with South African football, there is nothing that they have investigated or found in relation to SAFA itself. This is a matter between FIFA and the referee, and they have investigated the referee we will respond later after we have studied all the letters".
This means that it's now back to square one for Bafana Bafana, who are bottom of Group D with a single point after three matches.
South Africa earned the point with a 1-all draw against Burkina Faso away from home, last October.
Danny Jordaan says, "It's ten months after the match, consistently over the ten months those three points were reflected in all the logs that FIFA put out, so this came as a surprise at the back of all of the matches which have been played on Wednesday. On Thursday there is a decision that has an impact on the results on top. But those are matters that our legal committee has to look at".
Bafana Bafana's chances of qualifying for Russia 2018 are virtually over, after they suffered two back to back losses against minnows Cape Verde this month.
Danny Jordaan says, "Of course we have to look at what went wrong and those two matches, certainly the team did not perform at the level we expected now we have to get the report from the technical staff and make the assessment as to what are the next steps of course the news from FIFA complicates the matter even further."