Edu Garcia (48th) doubled ATK's lead before Nerijus Valkis (69th) pulled one back for two-time winners Chennaiyin.
But deep into second half stoppage time, Garcia -- who had not found the back of the net before the final -- rounded goalkeeper Vishal Kaith after being teed up by Pronay Halder to score and break into wild celebrations.
Due to the coronavirus outbreak, the final had to be played behind closed doors. There were however about 200 people in the stadium as part of the organisers, media, and security inside the stadium besides the players and officials.
But there was no dearth of intensity as both teams looked eager to break the deadlock as early as possible.
Chennaiyin had the first chance to nose ahead in the fourth minute when Valkis' effort came off the crossbar from close range.
ATK broke the deadlock as Hernandez scored his first goal of the season.
John Johnson sent a long ball for Roy Krishna who whizzed past Eli Sabia on the left side of the box to drill a cross which David Williams dummied for Hernandez to score brilliantly on the half volley.
Hernandez could have added to his tally in the 23rd minute but a superb goal line clearance by Laldinliana Renthlei saved Chennaiyin their blushes.
At the other end, Malta striker Andre Schembri forced Arindam Bhattacharya into an acrobatic save just after the half-hour mark from a Rafael Crivellaro free kick.
ATK were dealt a body blow five minutes before halftime when Krishna had to be substituted after he clutched his left hamstring in pain and could not continue. The Fiji striker was replaced by Armando Pena.
ATK doubled their advantage soon after the interval. Garcia found David Williams with a long ball. The Australian forward beat Sabia on the left flank to square the ball back to Garcia for the Spaniard to enter the box and slot home from close.
The second goal spurred Chennaiyin to life as ATK looked to sit back and defend their two-goal cushion. Lallianzuala Chhangte shot just wide of goal in the 52nd minute before Habas took off Regin M for holding midfielder Pronay Halder.
Owen Coyle's side were rewarded for their industry up front. Laldinliana played a one-two with Anirudh Thapa before floating a cross inside the box. Pritam Kotal's poor clearance fell to Jerry Lalrinzuala who sent the ball to Valskis with the Lithuanian finding the back of the net.
Valskis had another golden chance to level the tie from close range but his header was saved well by Bhattacharya under the bar.
For ATK, Garcia was one-on-one with Vishal Kaith but the young Chennaiyin goalkeeper came out of his line in time to avert the danger.
It was end to end till the dying minutes of the match before Garcia sealed the deal with a crisp finish.