Fast bowler Umesh Yadav was also shown the door.
Manish Pandey, who was left out of the squad for the three-match T20 series in Australia, which India won 3-0, was included in place of Gurkeerat Singh Mann.
Bhuvneshwar Kumar also made a comeback to the T20 team after recovering from a fractured left thumb, sustained during the fourth ODI against Australia in Canberra last month.
Kohli was in superb form during the Australia T20 series, scoring 199 runs in three matches, including three half-centuries, to steer India to a 3-0 whitewash.
Delhi's 23-year-old spinner Negi's inclusion ahead of Axar Patel is a surprise, considering the former did not do much with the ball for Delhi in the Mushtaq Ali Trophy T20 matches.
He claimed just six wickets in nine matches, giving away over eight runs per over, but proved handy with the bat, scoring 173 runs.
The three matches in the series against Sri Lanka will be played in Pune (February 9), Ranchi (February 12) and Visakhapatnam (February 14).
India: Mahendra Singh Dhoni (Captain), Rohit Sharma, Shikhar Dhawan, Ajinkya Rahane, Manish Pandey, Suresh Raina, Yuvraj Singh, Hardik Pandya, Ravindra Jadeja, Ravichandran Ashwin, Jasprit Bumrah, Ashish Nehra, Harbhajan Singh, Bhuvneshwar Kumar, Pawan Negi.
Image: Virat Kohli
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