Mbombela - SAFA said on Sunday they had lodged an appeal with the Confederation of African Football (CAF) regarding the outcome of the 2012 Africa Cup of Nations qualifying competition.
South Africa, who held a superior goal difference, picked up nine points in the qualifiers, leaving them level with Sierra Leone and Niger, while Egypt were left trailing in last place.
According to CAF rules, Bafana were eliminated, while Niger progressed with a better head-to-head record, having beaten South Africa and Sierra Leone.
South Africa played to a goalless draw against Sierra Leone in Nelspruit on Saturday in a match that preceded a whirlwind of confusion.
Bafana players and officials celebrated, under the impression they had qualified for the continental tournament before learning they had been knocked out.
"SAFA has lodged an appeal with the Confederation of African Football (CAF) regarding the outcome of qualification for the 2012 Africa Cup of Nations tournament to be held in Equatorial Guinea and Gabon," read a statement from the association.
After drawing 0-0 with Sierra Leone at Mbombela Stadium on Saturday, and with Niger losing 3-0 to Egypt in a simultaneous fixture, it meant Bafana topped the group followed by Sierra Leone and then Niger - all on nine points.
However, Niger qualifies in accordance with chapter 14 of the CAF competition regulation rules that the body had to explain on their website on Saturday evening with both South Africa and Niger celebrating and claiming qualification after their respective ties.
Article 14.1 says the team with greater number of points obtained against the "concerned teams" qualifies.
This means that with results against bottom-placed Egypt not counting, Niger goes through having beaten both Sierra Leone and Bafana, giving them six points.
Even the Leone Stars coach Lars Mattsson was confused after the match as he congratulated his Bafana counterpart Pitso Mosimane for progressing through to next year's continental showpiece.
Mosimane corrected Mattsson when it was his turn to speak in the post-match conference, saying: "We don't know whether we have qualified, we are not sure about the situation.
"South Africa deserves to be in next year's Afcon. I'm confused, but if we didn't qualify it will be a sad story," he ranted. "Put points on the table now and tell me are you going to put Niger on top now even with our better goal difference?"
While it is not known whether CAF will consider the appeal, SAFA will have to deal with the rule in question in their 2014 World Cup qualifiers and possibly in Baby Bafana's final group qualifiers for next year's London Olympics.
While Bafana will host the 2013 Afcon tournament, they will start their World Cup qualifiers in June next year. They have been drawn in Group A alongside Botswana, Central African Republic, Somalia or Ethiopia, with the final matches set for September 2013.
Coach Shakes Mashaba's Under-23s will compete in the first ever CAF Under-23 championships set for Egypt from November 26 to December 10 to determine whether they go to the 2012 London Olympics. The chapter 14 rule might once again be a factor.
They are in Group A alongside Egypt, Gabon and Ivory Coast.
The finalists and winners of the third and fourth place match will advance to the Olympics and the fourth placed side will play-off against an Asian Football Confederation (AFC) country.