Kohli was accompanied by team manager Ravi Shastri at the service in Hughes' hometown of Macksville.
Hughes, 25, died on Thursday two days after being struck on the neck by a ball during a domestic cricket match.
His tragic death has prompted the rescheduling of Australia's upcoming Test series with India.
Instead of starting in Brisbane on Thursday, the series will now begin in Adelaide on 9 December.
The changes have been made because of welfare concerns for Australia's players grieving for Hughes.
Around 1,000 people packed into Macksville High School, which Hughes attended, for the 80-minute service as thousands more watched on screens outside
Kohli, along with Shastri and Indian coach Duncan Fletcher, joined cricketers from around the world in the funeral procession after the service.
Indian Prime Minister Narendra Modi tweeted that Wednesday's service was "heart rending":
And Sambit Bal, editor of ESPNcricinfo.comâ€Ž, tweeted that Hughes "died doing what he loved the most":
Indian players, including cricket legend Sachin Tendulkar have paid rich tributes to Hughes in the days after his death.
Batsman Ambati Rayudu, who played with Hughes in the IPL team Mumbai Indians, described his death as "tragic".
"He was always smiling and was a tough competitor. He was very friendly and you can say he was the nicest Australian I knew," Rayudu told The Times of India newspaper.
Indian captain Virat Kohli has joined  mourners at the funeral of Australian cricketer Phillip Hughes in New South Wales.