Hardik Pandya's inclusion at the expense of Bhuvneshwar Kumar is the sole change in the 15-man squad that whitewashed West Indies earlier this month
India wicketkeeper MS Dhoni's absence from the side has continued after he was left out of the T20I squad for the series against South Africa.
Dhoni, who missed the 3-0 whitewash of West Indies in the 20-over format earlier this month, has not played for India since their defeat to New Zealand in the semi-finals of the 50-over World Cup.
The only change to the squad from the West Indies series is the reintroduction of allrounder Hardik Pandya, who comes in at the expense of fast bowler Bhuvneshwar Kumar.
Pandya, 25, was omitted from the squads for all three formats against West Indies after a gruelling year which has seen him play in tours of Australia and New Zealand, as well as the Indian Premier League and World Cup.
Jasprit Bumrah, who was also rested for India's white-ball games in the USA and Caribbean, has also been left out, which has resulted in Virat Kohli going in with an inexperienced fast bowling trio of Navdeep Saini, Deepak Chahar and Khaleel Ahmed.
India's first T20I against the Proteas takes place on September 15 in Dharamsala.
India T20I squad for three-match series against South Africa
Virat Kohli (c), Rohit Sharma, Shikhar Dhawan, KL Rahul, Manish Pandey, Shreyas Iyer, Rishabh Pant, Krunal Pandya, Hardik Pandya, Ravindra Jadeja, Washington Sundar, Rahul Chahar, Khaleel Ahmed, Deepak Chahar, Navdeep Saini