Peterson will replace batsman Hashim Amla in the squad that is now preparing for the limited-overs section of their tour of England. South Africa won the Test series 2-1.
"Considering the tournament takes place on the sub-continent the selection committee has opted for two spinners," Cricket South Africa chief executive Gerald Majola said in a statement.
"Having a left and right-arm option in Robin Peterson and Johan Botha gives the selectors the variation they're looking for," added Majola, who is acting as convenor of the selection panel after the recent resignation of Joubert Strydom.
Off-spinner Botha has played 27 one-day internationals. Peterson has featured in 35 ODIs but was last used at the 2007 World Cup in the Caribbean.
Second-seeded South Africa play England, New Zealand and Sri Lanka in Champions Trophy Pool B, with the top two going through to the semi-finals.
Squad: Graeme Smith, Johan Botha, Mark Boucher, AB de Villiers, JP Duminy, Herschelle Gibbs, Jacques Kallis, Albie Morkel, Morne Morkel, Andre Nel, Makhaya Ntini, Justin Ontong, Robin Peterson, Vernon Philander, Dale Steyn.
(Reporting by Ken Borland, editing by Tony Jimenez)