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GALLERY: Past weekend's sporting pictures
SAFA president Kirsten Nematandani announced on Monday he had vacated the post to his deputy, Mwelo Nonkonyana, who would act as interim chairman until a replacement was found before the end of the month.
Nematandani said he could not be a "referee and player" and refuted claims that he had been toppled from the AFCON local organising committee (LOC) chairman's post while he was in London, England, last month.
"As SAFA president, I can't report to myself," Nematandani said.
"First option was to have the LOC under SAFA before it was decided to be independent.
"Yes, I went to London, but it was after a board meeting where everything was agreed upon."
The LOC also clarified the much debated bidding process that saw Cape Town excluded from the five cities that will stage the continental showpiece early next year.
The City of Cape Town had raised queries regarding the costs of hosting matches.
Cape Town Mayor Patricia de Lille said in a statement last week the city, which boasts the Cape Town Stadium, a 2010 World Cup venue, was "disappointed" not to have been named as an AFCON host.
Nematandani, however, said other cities had produced more enticing bids, with Mbombela, Port Elizabeth, Rustenburg, eThekwini and Johannesburg getting the nod.
"It was not a blunder to leave Cape Town out," said LOC chief executive Mvuzo Mbebe.
"It was what [other] cities proposed to us as their plans."
Cape Town was named with Polokwane, Kimberley and Bloemfontein as host cities for the 2014 African Nations Championships (Chan).
"We have no doubt built a good rapport with Cape Town ahead of them hosting Chan," Nematendani said.
