This is the first-ever win by any home team in the tournament in 13 years.
Coal India took the lead in the 11th minute from a goal scored by Dipak Ghatuar.
Partha Pratim Gogoi equalised for the local league champions in the 21st minute. Chetia scored two more goals in the 30th and 45th minutes to give Nepathya the lead.
In the second half of the match, the Coal India men made a comeback after the Nepathya team was reduced to 10 following a red card shown to Sailen Saikia.
Issac Tirkey and Bijoy Gohain pumped in two more goals for Coal India in the 68th and 79th minutes respectively to restore parity. However, Chetia scored the winning goal in the 86th minute to help Nepathya book a place in the second round.
Tinsukia Railway Divisional Sports Club will meet 9 Assam Police Battalion, Barhampur tomorrow.