Pienaar, who succeeded Aaron Mokoena as skipper after the 2010 FIFA World Cup™, revealed his decision in a letter to the association, which was read out ahead of a national squad announcement.
The slightly-built 30-year-old midfielder, the only South African footballer featuring regularly in a major European league, said he could no longer cope with the physical demands of playing for both his club and country.
"I am very disappointed as Steven was set to play a huge role going forward," recently appointed South Africa coach Gordon Igesund told a Johannesburg media conference.
"Steven says his body is tired and we must respect that decision - he has contributed a lot to the national team over the past ten years and we will miss him."
Igesund stressed that the door had not been slammed shut on Pienaar, who made a successful return to the Toffees this season after an unhappy spell at Tottenham Hotspur.
"If he has a change of mind and is fitter, stronger and better than his rivals for a squad place, he will be considered," said the coach, who won the South African Premiership title with a record four clubs.
"However, no footballer is guaranteed a place in the South African squad - not even [Lionel] Messi or [Cristiano] Ronaldo, if they were available to play for this country."