The Abhishek Bachchan co-owned side had finished runners-up behind the Blues in the regular season. Chennaiyin then beat FC Goa over two legs in the playoffs and emerged victorious over the ISL newcomers in the final, played at the latter's home ground to lift their second title.
The Machans, who earlier lifted the trophy in 2015, equal ATK's haul of two titles, joining the Kolkata side as the joint most successful club in the league, which began in 2014.
The side, who ended their three-season old relationship with former coach Marco Materazzi after a dismal 2016 season, finishing 7th, tasted success immediately under the tutelage of former Aston Villa manager John Gregory.
As many as seven survivors from the first triumph win their second piece of silverware with the club. Karanjit Singh, Dhanapal Ganesh, Mailson Alves, Raphael Augusto and Jeje Lalpekhlua all started on the night with Thoi Singh and Dhanachandra Singh the other members of the victorious 2015 squad.
Chennaiyin FC also become the first ISL side to book a place in next season's AFC Cup play-off after the Asian Football Confederation allotted one of India's continental spots to the ISL winner.