The three Proteas named are Hashim Amla, Jacques Kallis and Dale Steyn. The others named in Wisden's Five are West Indies all-rounder Marlon Samuels and South African-born England opening batsman Nicholas Compton.
Previous Wisden triples from South Africa were Graeme and Peter Pollock and Colin Bland in 1966 and Dale Benkenstein, Mark Boucher and Neil McKenzie in 2009.
"Hashim Amla was the batting sensation of the summer, gracefully compiling South Africa's first Test triple-century, and top-scoring in eight international innings out of 11," said Wisden Editor Lawrence Booth.
"Dale Steyn cemented his status as the world's most frightening fast bowler, blowing England away on the final afternoon at The Oval, then undermining them in the Third Test at Lord's."
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Cricket South Africa (CSA), lauded the three Proteas for their achievement.
"What a wonderful way for a South African celebration of the 150th edition of this famous publication - known affectionately as the 'cricketer's bible'," said CSA Acting CEO Naasei Appiah.
"It has truly been a phenomenal year for our Proteas and they have been and will continue to be an inspiration to the nation."
Graeme Smith, captain of the victorious 2012 squad that received the International Cricket Council Mace as world's best Test team a fortnight ago, won the Wisden honour in 2004.