Kohli scored his first one-day international hundred since February in Dharmasala as India reached 330-6 in their 50 overs, with Suresh Raina (71) and Ajinkya Rahane (68) also providing important contributions.
The 25-year-old had gone nine ODI innings since last reaching three figures against Bangladesh and, although he had some fortune when he was dropped on 99, he anchored India's innings, something that earned praise from his captain.
"Virat played well in the last game," Dhoni said. "He continued from there and it's important he gets back into good nick.
"He took his time, normally he is naturally aggressive. I thought he would attack the spinners, but he took his time and built his innings."
After losing an early wicket the West Indies found themselves behind the run rate and, despite Marlon Samuels making 112 from 106 balls, they were bowled out for 271, giving India a 2-1 lead in the series.
Dhoni felt his side should have scored more, though.
"A few more runs would have been good," he added. "When we were going back to the hotel yesterday, we thought we would want 350-360.
"But we did well with the new ball, Bhuvi [Bhuvneshwar Kumar] bowled really well."
Kolkata is due to host the final match of the series on Monday, but the future of the series remains in doubt after conflicting statements were released by the Board of Control for Cricket in India and West Indies Cricket Board over the tourists pulling out of the tour.