Gill has still not recovered from the neck spasms he suffered in the first Test against South Africa in Kolkata.
Rohit and Kohli have both retired from T20I and the Test formats and last featured for India in the 50-over series in Australia last month.
Rishabh Pant is also back in the ODI mix as the second wicketkeeper, having last played the format in August 2024.
Fast bowlers Jasprit Bumrah and Mohammed Siraj has been rested for the ODIs and will likely return for the five-match T20I series that will follow.
Arshdeep Singh, Prasidh Krishna and Harshit Rana are the seam-bowling options selected while Yashasvi Jaiswal is expected to open the batting in Gill's absence.
Shreyas Iyer remains unavailable as he continues to recover from a lacerated spleen suffered in Australia.
The three ODIs between India and South Africa will be played on November 30 in Ranchi, December 3 in Raipur and on December 6 in Visakhapatnam.
India's ODI squad: KL Rahul (captain), Rohit Sharma, Yashasvi Jaiswal, Virat Kohli, Tilak Varma, Rishabh Pant (wk), Washington Sundar, Ravindra Jadeja, Kuldeep Yadav, Nitish Kumar Reddy, Harshit Rana, Ruturaj Gaikwad, Prasidh Krishna, Arshdeep Singh, Dhruv Jurel
The Proteas are on the brink of a historic series victory in India after batting the home side out of the contest on the fourth day of the second and final Test in Guwahati.
Marco Jansen took six wickets as the Proteas enjoyed a near-perfect third day of the second Test against India with the tourists sniffing a historic series victory.
All-rounder Senuran Muthusamy scored his maiden Test ton (109) and Marco Jansen smashed a brisk 93 (91) to boost South Africa to 480 all out on Day Two of the second Test.
The Proteas will lament a few soft dismissals as they went to stumps on day one of the second and final Test against India on 247-6 as they chase a historic series victory.
