Javier Hernandez (10') and Edu Garcia (48') put ATK in the driving seat but Nerijus Valskis (69') reduced their advantage to set up a tense end to the contest. Hernandez scored another in injury time (90+4') to confirm a record third title.
The final was off to a blistering start as Andre Schembri made a good run to the byline on the right in the first minute and found Rafael Crivellaro in the centre with a good cross, but the Brazilian mishit his effort. Schembri threatened again minutes later, this time with a pass to Valskis whose shot hit the crossbar.
ATK drew first blood with their first major sight of goal in the 10th minute. John Johnson's cross-field ball found Roy Krishna on the left flank who delivered a good cross towards the edge of the box. Javier Hernandez, who was left unmarked, smashed a half-volley into the ground and beat goalkeeper Vishal Kaith to give ATK the lead.
The contest remained open but Chennaiyin suffered an injury setback midway through the first half. Midfielder Germanpreet Singh had to be replaced and Edwin Vanspaul took his place.
ATK went close to doubling their lead in the 23rd minute out of utter chaos inside the box which produced three back-to-back attempts. Krishna cut in from the right and unleashed a powerful strike which was saved by Kaith. Javier Hernandez then had the ball at his feet twice, but on both occasions, his shot was blocked.
Chennaiyin put pressure on the ATK defence and carved out a golden chance from a free-kick after the 30-minute-mark. Schembri met Crivellaro's delivery into the box but Arindam Bhattacharya pulled off an excellent save to keep ATK's lead intact.
The scoreline remained 1-0 in favour of ATK at the break, but the Kolkata side had a concern of their own as Krishna had to be replaced by Mandi Sosa due to an injury.
ATK scored the all-important second goal and doubled their advantage two minutes into the second half. Williams picked up the ball in midfield and fed Edu Garcia into the box. The Spanish midfielder beat Kaith with a neat finish from an acute angle to make it 2-0.
The Chennaiyin attack struggled to create clear-cut chances and their opponents restricted them to long-range efforts. Lallianzuala Chhangte attempted a piledriver from outside the box before the hour mark but sent the ball wide.
Chennaiyin finally found a way past the ATK defence in the 69th minute. Laldinliana Renthlei played a neat one-two with Anirudh Thapa on the right before sending a cross into the centre of the box. Pritam Kotal's headed clearance fell to Jerry Lalrinzuala who passed the ball to Valskis in the centre. The Lithuanian striker found the net with a powerful strike to score his 15th goal of the season and give Chennaiyin a lifeline.
Chennaiyin built one attack after another as the game neared full-time but the balls into the box were well dealt by ATK.
ATK got their third goal of the night and struck the final blow in the last minute of injury time. Substitute Pronay Halder lifted the ball over the Chennaiyin defence into the path of Hernandez who slotted the ball home.