Cricket South Africa (CSA) also announced that it would include a number of young players to give them an opportunity to show their mettle in the series.
De Villiers, who quit as Proteas Test captain last year, will lead the T20 side in the absence of regular captain Faf du Plessis, who has a niggling shoulder injury and has returned home to be with his wife Imari for the birth of their first baby.
"We are indeed fortunate in the quality of our team leaders and Farhaan remains very much part of this group," Zondi said.
"We have also been impressed as a panel by the quality of players coming through our franchise and South Africa 'A' system and we are ready to give further opportunities to Andile Phehlukwayo, Mangaliso Mosehle, Jon-Jon Smuts and Dane Paterson who all made their debuts in the recent series against Sri Lanka. Unfortunately, Lungi Ngidi could not be considered because of injury," Zondi added.
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There is one new cap in this format in Dwaine Pretorius, who has been a regular member of the ODI squad during the past season.
The three games will be played on June 21 in Southampton; June 23 in Taunton and June 25 in Cardiff.
South Africa T20 Squad: AB de Villiers (captain), Farhaan Behardien; Reeza Hendricks; Imran Tahir; David Miller; Morne Morkel; Chris Morris; Mangaliso Mosehle; Wayne Parnell; Dane Paterson; Andile Phehlukwayo; Dwaine Pretorius; Tabraiz Shamsi; and Jon-Jon Smuts.