Duminy will lead the side in absence of injured Faf du Plessis, who fractured his index finger in the first ODI at Durban.
Stand-in skipper Aiden Markram and senior batsman Hashim Amla have been rested for the series.
Leg spinner Imran Tahir too has been left out, although chief selector Linda Zondi said that he has just been rested to give left arm spinners Tabraiz Shamsi and Aaron Phangiso more game time.
Fast bowlers Morne Morkel, Kagiso Rabada and Lungi Ngidi have also been rested owing to the heavy workload this home summer.
South Africa T20 squad: JP Duminy (capt), Farhaan Behardien, Junior Dala, AB de Villiers, Reeza Hendricks, Christiaan Jonker, Heinrich Klaasen, David Miller, Chris Morris, Dane Paterson, Aaron Phangiso, Andile Phehlukwayo, Tabraiz Shamsi, Jon-Jon Smuts.
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