Prasad's much talked about tenure as chairman of Indian Men's selection panel ended on March 4.
The big change took place three years ago when Dhoni relinquished his post officially from ODIs and T20Is, having retired as a player from Test cricket in December 2014.
Kohli has since been a successful leader of the side across formats, especially in Tests where the Indian team currently reigns supreme in the World Test Championship.
Read Also: MSK Prasad wants selectors to have a say in playing XI on away tours
"I personally feel that my colleagues and I can take pride in the fact that we have successfully seen the transition period from MSD to Virat very well," Prasad told Mid-Day. "Once Mahi completed his [captaincy] stint, we had to look at somebody who could step into those shoes. We wanted to see that happening smoothly. Once Virat took over, we reached the No. 1 ranking across all three formats. That's the biggest satisfaction I got."
Dhoni hasn't played for India post the end of the last year's World Cup in UK, since when there have been widespread speculations over the great wicketkeeper batsman's retirement. Prasad, however, said Dhoni had communicated his future plans with him and the team management.
"MS is clear about his future which he expressed to me and the team management," he said. "I cannot disclose details as it is confidential. It's best that whatever discussed and shared between us [selection committee and the team management] remains there. It's an unwritten code."
The selection committee was criticised for being partly responsible for the middle-order muddle that India stepped into the last year's World Cup with.
"I don't really see that the position of No. 4 as the reason for not winning the World Cup," he said. "If you have topped the table prior to the semi-final, that speaks volumes of the team. So, one cannot say that because of the No. 4 position [we lost the World Cup]."
Prasad's tenure was full of talks around his lack of experience as a former Test cricketer and how he might be intimidated into making selection calls as per the demands of the team management.
But the man leaves behind him some fantastic work done on India's bench strength, which if backed with better talent identification and consistent policy by those responsible of picking the playing XI, will serve the Indian team well in the years to come.
(Inputs from Mid-Day)