The skipper appeared to be struggling during Sunday's one-wicket defeat to the hosts and did not field as his side failed to defend a target of 229.
And the BCCI have now confirmed that Dhoni will take no further part in the action in the Caribbean, with Ambati Rayudu called up as his replacement and Kohli installed as skipper.
Following the defeat to the hosts, Kohli admitted that India missed the presence of their captain in the field but insisted he was perfectly happy to stand in.
"There were times when you are under pressure and you miss him because he remains calm under pressure," he said. "I have captained in the IPL but that's a Twenty 20 game. This was totally unexpected. It was more thinking on the feet. It was a good experience for me."
Dinesh Karthik kept wicket in the absence of Dhoni on Sunday and is likely to continue in the role, with Murali Vijay the most likely candidate to take the captain's spot in the batting line-up. The pressure will be on in Kingston with both sides knowing that defeat would leave them a big mountain to climb to reach the final.
The Windies had already claimed a bonus point while defeating Sri Lanka in the tournament opener before they beat the Champions Trophy winners and are in firm control of the group.
One more win will see the hosts into the final meaning that the results of the matches between the two other teams are likely to decide which of them will face Dwayne Bravo's men in the showpiece clash.
Sri Lanka are likely to be unchanged as they look to bounce back from Friday's convincing six-wicket defeat.
Mahela Jayawardene scored 52 from the unusual position of opener in that match and, while captain Angelo Mathews also managed a half-century, no batsman outside of the top five managed to reach double figures.