Fast bowler Jasprit Bumrah will be vice-captain for the series.
India opener KL Rahul has been named captain for the three-match one-day international (ODI) series in South Africa with newly-appointed skipper Rohit Sharma still unavailable due to injury, the Indian board's (BCCI) selectors said on Friday.
Rohit, who replaced Virat Kohli as India's white-ball skipper earlier this month, picked up a hamstring injury during a training session in Mumbai ahead of the South Africa tour.
Fast bowler Jasprit Bumrah will be vice-captain for the series. Fellow seamer Mohammed Shami has been rested while Axar Patel and Ravindra Jadeja remain unfit.
"We decided that Rohit should work on his fitness with so much cricket," Chetan Sharma, chairman of the selection committee, told reporters.
"We had a good chat with Rohit and that's the reason he is not going to South Africa and Rahul is captain."
Kohli, who relinquished the Twenty20 captaincy, was removed as India's ODI skipper as well because the selectors did not want to have two different white-ball captains.
Chetan said Kohli's decision to step down as T20 captain came as a surprise with another World Cup on the horizon next year, adding that the selectors had urged him to reconsider and continue as captain before eventually accepting his decision.
"Everybody told him to think about it ... The main aim for everybody, the goal is the same - to get India on top," Chetan added.
"It was a hard decision for the selectors, but selectors have to take hard decisions ... I know Virat is an important player for us in the coming days and coming years."
The ODI series begins on January 19 after the test series in which India lead 1-0. The second test begins on January 3.
KL Rahul (captain), Shikhar Dhawan, Ruturaj Gaekwad, Virat Kohli, Shreyas Iyer, Surya Kumar Yadav, Venkatesh Iyer, Rishabh Pant (wicketkeeper), Ishan Kishan (wicketkeeper), Ravichandran Ashwin, Yuzvendra Chahal, Washington Sundar, Jasprit Bumrah (vice-captain), Bhuvneshwar Kumar, Deepak Chahar, Prasidh Krishna, Shardul Thakur, Mohammed Siraj