The BCCI has deputed its general manager MV Sridhar to supervise the team management for the West Indies tour.
In 17 Tests, Kumble saw India win a dozen, drawing four and losing just one against Australia.
India even retained the No 1 spot in Test ranking under Kumble's term.
India cricket coach Anil Kumble on Tuesday stepped down from his position after a widely-speculated feud with captain Virat Kohli, marking a bitter end to a highly successful tenure.
"The Board of Control for Cricket in India (BCCI) confirms that Anil Kumble has withdrawn his services as the post of the Head Coach for the Senior India Men’s team," a statement from the BCCI read.
"While the Cricket Advisory Committee had endorsed an extension to his tenure as Head Coach, Anil Kumble has decided not to continue as the coach," read the statement further.
Meanwhile, BCCI acting president C K Khanna and acting secretary Amitabh Choudhary thanked Kumble for his services to the Indian team.
"We wish to place on record our sincere appreciation for the immense contribution by Anil Kumble to the team which enabled India to attain the No.1 Test position. Indian cricket needs his continued contribution in various capacities and wishes him all the best in his future endeavour," said Choudhary.
Kumble's decision comes in the wake of reports claiming rifts between him and Kohli, and just two days after India's embarrassing loss to Pakistan in the Champions Trophy final.
His one year contract expired at the end of the Champions Trophy but he was given the option to travel with the team to the West Indies for the limited overs series beginning on Friday.
However, Kumble decided to stay back in London for the ICC 'Annual Conference' as he is the chairman of the Cricket Committee, while the Indian team boarded the flight to Barbados.
Kohli had met the BCCI top brass along with Kumble in London before leaving for the West Indies on Tuesday. The meeting took place after the high-profile Cricket Advisory Committee (CAC) communicated to the BCCI that it had failed resolve the differences between Kumble and Kohli.
The BCCI had invited fresh applications for the post of head coach days before the start of Champions Trophy.
Kumble was a direct entry into the coach selection process while the others who applied for the post were Virender Sehwag, Tom Moody, Richard Pybus and Lalchand Rajput among others.
On the sidelines of the Champions Trophy in the UK, the CAC comprising Sachin Tendulkar, VVS Laxman and Sourav Ganguly held meetings with Kumble as well as Kohli to sort out the differences between the two.
It was being widely perceived in the BCCI that in the meeting between Kohli and CAC, the skipper had made it clear that his relationship with the coach had reached a dead end.
It was only the CAC which had picked Kumble as the coach last year. It has been learnt that the committee will soon have a conference call to decide on Kumble's successor.
"The BCCI will continue to seek the assistance of the Cricket Advisory Committee in its search for a new Head Coach for the Senior India Men's Cricket Team," said the BCCI statement.
"In the interim, the BCCI has deputed MV Sridhar, GM - Cricket Operations to supervise the team management for the West Indies tour," it said further, adding that batting coach Sanjay Bangar and fielding coach R Sridhar will remain with the Indian team in the West Indies.
Notably, during the entire Champions Trophy, there was hardly any communication between the two during the practice sessions with Kumble mostly keeping to himself or giving some practice to the bowlers.
The team did well under Kumble in the past 12 months, winning Test series in the West Indies (2-0) before winning at home against New Zealand (3-0), England (4-0), Bangladesh (1- 0) and Australia (2-1).
The team won eight ODIs and lost five during the 46-year-old's tenure.
Image: Anil Kumble
Photograph: Peter Cziborra/Reuters