Bolstered by Shai Hope and then the finishing kick by Ashley Nurse, bolted West Indies to 283 in their 50 overs.
Kohli, while leading the India run chase, pulled down a short ball to fine leg for a single to reach the feat off 110 balls with the help of ten fours and a six in the 38th over.
Part-time spinner Marlon Samuels claimed three wickets while skipper Jason Holder, fellow paceman Obed McCoy and spinner Ashley Nurse took two each.
Squad: Virat Kohli (captain), Murali Vijay, Lokesh Rahul, Prithvi Shaw, Cheteshwar Pujara, Ajinkya Rahane (vice-captain), Hanuma Vihari, Rohit Sharma, Rishabh Pant, Parthiv Patel, Ravichandran Ashwin, Ravindra Jadeja, Kuldeep Yadav, Mohammed Shami, Ishant Sharma, Umesh Yadav, Jasprit Bumrah, Bhuvneshwar Kumar.
Currently, Black History Month is being observed in the West Indies and Africa to recognise the contribution of the black soldiers during the First and Second World wars. Just when the partnership looked settling, Hetmyer, while trying to go big, missed the ball before Mahendra Singh Dhoni made no mistake in dislodging his bails, leaving the visitors reeling at 111/4.
India did not get the best of the starts as they lost Rohit Sharma in the second over itself.
After an easy 8-wicket sailing in the series opener in Guwahati, India were denied a comfortable 2-0 lead in the five-match rubber as the tourists managed to salvage a morale-boosting tie in the second ODI at Visakhapatnam. Samuels finished with figures of 3.4-1-12-3.
"We hung in the game, which was very important, " West Indies captain Jason Holder said. For India, pacer Jasprit Bumrah scalped four wickets in his comeback match.
Earlier, Jasprit Bumrah - one of the three fast bowlers the hosts drafted in for the match - was the pick of the Indian attack with four for 35, and his early strikes threw the West Indies' innings into disarray.
India chose to bowl in the third ODI against West Indies in Pune.