Kohli is captain of the team currently playing in a tri-series in the Caribbean in the absence of regular skipper Mahendra Singh Dhoni, who went home after the first match due to a hamstring injury.
The India selectors decided to rest offspinner Ravichandran Ashwin and pace bowlers Ishant Sharma, Umesh Yadav and Bhuvaneshwar Kumar.
Opener Murali Vijay was also not picked for the low-profile tour.
Offspinner Parvez Rasool became the first player to be picked for a national squad from the northern state of Jammu and Kashmir while pace bowler Mohit Sharma was the other new name in the squad for the five one-day internationals starting on July 24 in Harare.