After being ruled out of the Test series with a left hamstring injury, the new white-ball skipper will miss the three 50-over matches in the New Year
India will be led by KL Rahul during next year's one-day international series in South Africa after Rohit Sharma was ruled out through injury.
A left hamstring problem had already taken Rohit out of the ongoing three-Test series.
But he hasn't been deemed fit enough to begin his permanent spell in charge of the white-ball sides, following Virat Kohli's decision to step down from both roles.
Rahul has never previously led India before in any format.
Jasprit Bumrah will act as vice-captain for the 50-over matches, which will form part of the Cricket World Cup Super League - thought hosts India have already qualified.
Following the second and third Tests, South Africa host India in three ODIs on January 19, 21 and 23, with the first two being at Paarl and the concluding game at Newlands.
India squad: KL Rahul (c), Shikhar Dhawan, Ruturaj Gaekwad, Virat Kohli, Surya Kumar Yadav, Shreyas Iyer, Venkatesh Iyer, Rishabh Pant (wk), Ishan Kishan (wk), Yuzvendra Chahal, Ravichandran Ashwin, Washington Sundar, Jasprit Bumrah (VC), Bhuvneshwar Kumar, Deepak Chahar, Prasidh Krishna, Shardul Thakur, Mohammed Siraj