South Africa lost out in a three-way tie in their qualifying group with unheralded Niger taking top spot because of a better head-to-head record when Bafana Bafana thought that goal difference was the deciding factor.
They are pressing ahead with their legal bid to try to overturn their failure to qualify for next year's finals, although critics have accused them of putting forward a flimsy argument to cover up their embarrassment.
"We are going ahead with an appeal to the Confederation of African Football (CAF) because we think we have a case," South African Football Association chief executive officer Robin Petersen told reporters.
Petersen said goal difference is a fairer option than head-to-heads and that there is past precedent to overturn the standings, even though the rules had been set out by CAF some time before the qualifiers even started.
Coach Pitso Mosimane (pictured) informed officials on Monday he had read the rules before Saturday's last qualifying game against Sierra Leone in Nelspruit but misinterpreted them, Petersen told Reuters.
The coach was called in to explain why he played for a 0-0 draw in a game that South Africa needed to win irrespective of the result in the other group match, where bottom side Egypt beat Niger 3-0 in Cairo.
The games were played simultaneously on Saturday.
Niger led both South Africa and Sierra Leone by a single point going into the weekend's last round of qualifiers but when news that Niger were trailing in Cairo reached Mosimane, he told his players to play for a draw believing it would be enough to qualify.
There was exaggerated timewasting in the final minutes followed by scenes of celebration before South Africa discovered they had botched the permutations.
A CAF spokesman said a South African protest would be looked into but refused further comment.
Mosimane, who took over as South Africa coach after the country's hosting of the 2010 World Cup, has taken the brunt of vitriolic condemnation on radio talk shows and across social media with a majority of fans calling for his dismissal.
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