Opener Rohit Sharma will lead a young Indian side in Twenty20 tri-series.
Kohli missed Saturday's final Twenty20 against South Africa in Cape Town with a stiff back as India won the three-match series 2-1 which followed their 5-1 triumph in the one-dayers against the Proteas.
Rohit led India during the final T20I against South Africa in Cape Town which his side won, and also captained India in the ODI and T20I series against Sri Lanka in December, both of which India won.
India have a long season ahead starting with the IPL before the team embarks on a long sojourn of England followed by a tour Down Under in December.
Former skipper Mahendra Singh Dhoni was also rested, which allowed Delhi`s Rishabh Pant to join the squad as the second wicketkeeper, along with Dinesh Karthik.
The selectors also decided to leave out the pace duo of Bhuvneshwar Kumar and Jasprit Bumrah and named a largely young 15-member squad for the Nidahas Trophy, which also features Bangladesh, beginning on March 6 in Colombo.
"We`ve kept in mind the workload and upcoming schedule while finalising the team for Nidahas Trophy," selection committee chairman MSK Prasad said in a statement.
"The high-performance team has suggested that adequate rest should be given to our fast bowlers to help improve athletic performance, maximise rest and prevent injury."
Wrist-spinner Kuldeep Yadav and all-rounder Hardik Pandya were also allowed a break following the tour of South Africa.
India squad: Rohit Sharma (captain), Shikhar Dhawan (vice-captain), KL Rahul, Suresh Raina, Manish Pandey, Dinesh Karthik (wicketkeeper), Deepak Hooda, Washington Sundar, Yuzvendra Chahal, Axar Patel, Vijay Shankar, Shardul Thakur, Jaydev Unadkat, Mohammad Siraj and Rishabh Pant (wicketkeeper)