
Pienaar was forced to leave his club-mates under FIFA's "14-day rule." Everton insisted the rule did not make it clear whether players should be released 14 days ahead of the start of the competition, or 14 days ahead of a specific country's first match.
The African Cup on Nations begins in Ghana on January 20, but South Africa do not play their opening game until January 23, when they face Angola in Tamale.
Manager David Moyes felt that common sense could have prevailed, as it has with the Nigeria players Joseph Yobo and Yakubu, both of whom will join their international squads after playing against Chelsea.
"The rules, in my view, do not stipulate exactly whether it is 14 days before the tournament or 14 days before South Africa's first game," said Moyes. "We have taken the latter view.
"We pay his wages, we pay him well and he is an employee of Everton and 14 days is more than enough time to prepare for the African Cup of Nations - which comes in the middle of our season.
"From my point of view as Everton manager, I fought tooth and nail for him. I was not going to let it go without a fight."
Pienaar was expected to fly to Pretoria Sunday, but Everton prevented him leaving and he trained with them Monday.
South Africa then appealed to FIFA, who intervened and insisted the player, who is on loan from germany's Borussia Dortmund, should be released.
"For the South African Football Association, our intention is not to punish the player, because the player is not to be blamed in this particular instance," a spokesman for the South African Football Association said.
"We've played the game by the rules, so FIFA will have to sanction the team."