Batsman Ambati Rayudu will be flown in as Dhoni's replacement.
"Mahendra Singh Dhoni has been ruled out of the ongoing tri-series in the West Indies, due to a hamstring injury. The All-India Senior Selection Committee has picked Ambati Rayudu as his replacement in the squad. Rayudu will join the team at the earliest," BCCI Secretary Sanjay Patel said in a statement.
"Virat Kohli will lead India in the remainder of the tri-series," the statement added.
Dhoni did not keep wickets against the West Indies during the team's tri-nation series opener in Jamaica yesterday after sustaining a hamstring injury while batting.
Dhoni handed over the wicketkeeping duties to teammate Dinesh Karthik in the match, which the West Indies won by one wicket at Sabina Park here.
The 31-year-old skipper, who led India's triumphant campaign at the ICC Champions Trophy, was to be examined by the doctors.
The Cricket Board sources had earlied said Dhoni was "not feeling good".
In Dhoni's absence, India's nine-match winning streak was brought to a halt, and they would look to get over the disappointment of a narrow loss when they take on familiar sub-continental foes Sri Lanka in their second match of the series tomorrow.