Kohli leads India in all three formats of the game and the 29-year-old has been in imperious form with the bat.
With India scheduled to travel to South Africa for a full tour immediately after the Sri Lanka series, the selectors decided to rest Kohli for the ODIs, which start on Dec. 10.
India won the second of the three-test series against the island nation by an innings and 239 runs in Nagpur on Monday and will play the final test in Delhi from Saturday.
Opening batsman Shikhar Dhawan returns to the squad for the final test after withdrawing from the second match for personal reasons.
India will also host Sri Lanka in three Twenty20 matches before embarking on the tour to South Africa.
India squad for third test:
Virat Kohli (captain), Murali Vijay, Lokesh Rahul, Shikhar Dhawan, Cheteshwar Pujara, Ajinkya Rahane, Rohit Sharma, Wriddhiman Saha (wicketkeeper), Ravichandran Ashwin, Ravindra Jadeja, Kuldeep Yadav, Mohammed Shami, Umesh Yadav, Ishant Sharma, Vijay Shankar
India squad for ODI series:
Rohit Sharma (Captain), Shikhar Dhawan, Ajinkya Rahane, Shreyas Iyer, Manish Pandey, Kedar Jadhav, Dinesh Karthik, MS Dhoni (wicketkeeper), Hardik Pandya, Axar Patel, Kuldeep Yadav, Yuzvendra Chahal, Jasprit Bumrah, Bhuvneshwar Kumar, Siddarth Kaul
(Reporting by Sudipto Ganguly; Editing by David Goodman)
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