The final was held without spectators owing to the COVID-19 pandemic.
The final of Indian Super League (ISL), scheduled to be held in Goa on March 14, will take place behind closed doors.
Bengaluru FC had won the first leg 1-0 but ATK's resurgence in the second leg saw them win the tie 3-2 on aggregate.
Two-time champions Chennaiyin FC booked their place in the final of the Indian Super League.
Deshorn Brown scored the only goal of the game as Bengaluru FC registered a 1-0 win against ATK in the first leg of their ISL semi-final.
Lucian Goian, Anirudh Thapa, Eli Sabia and Lallianzuala Chhangte scored as Chennaiyin FC defeated FC Goa 4-1 in the first leg of the ISL semifinal.
Lallianzuala Chhangte scored a late equaliser to secure a 2-2 draw against NorthEast United to finish fourth in the table.
ISL: Goa had last hosted the ISL final in 2015 played out between Chennaiyin FC and FC Goa, with the latter losing 2-3 in a dramatic fashion, after leading 2-1 till 90 minutes.
Bengaluru FC ended their league stage campaign with 30 points and could possibly finish fourth, should Chenniayin FC win their final league game against NorthEast United.
Chennaiyin FC qualified for the Indian Super League (ISL) playoffs with a 1-0 win at the Mumbai Football Arena.
Hyderabad needed three points to avoid being the worst team in the history of ISL and they were out to prove a point right from the kick-off.
Indian clubs like Mohun Bagan and East Bengal have played in the Asian Club Championships but no team from the country has ever played in the group stage of AFC Champions League since its introduction in 2002.
Chennaiyin FC are now just a point behind Mumbai City FC who are fourth on the table.
Kerala Blasters picked up their first win against Bengaluru FC in the Indian Super League (ISL) with a 2-1 result at the Jawaharlal Nehru Stadium on Saturday.
Odisha FC kept their hopes for a playoff spot alive with their 2-1 win over NorthEast United.
A brace from Ferran Corominas, a Mohammed Rafique own goal and goals from Hugo Boumous and Jackichand helped FC Goa secure a 5-2 win.
Three goals, a saved penalty and a red card in a dramatic last 10 minutes saw NorthEast FC and Jamshedpur FC play out a 3-3 draw.
Kerala Blasters FC are eighth on the table with 15 points while NorthEast United FC, who have not scored for five games in a row now, are a spot below with 12 points.