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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.
Batsman Christiaan Jonker has been included in the squad while keeper-batsman Heinrich Klaasen has also been called up to the T20 team for the first time, along with fast bowler Junior Dala.
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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.