William Asiedu Opoku scored the game's only goal in the 15th minute off a Chencho Gyeltshen assist at the Tau Devi Lal Stadium.
The club is only in its second season in top-flight football.
Minerva Punjab entered the final day's game with 32 points from 17 matches, and they were closely followed by Neroca FC, Mohun Bagan and east Bengal.
They are the second side from Punjab to win the top prize, the erstwhile JCT having won the inaugural National Football League in 1996-17.