As expected, the home side came out all-guns-blazing, chasing a three-goal deficit from the first leg. The Gaurs were boosted by the return of Hugo Boumous and Brandon Fernandes from injuries but the first goal of the match came from an unlikely source.
Goa launched one attack after another right from the off and a good cross from the right flank by Jackichand Singh in the 10th minute undid the visitors' defence. Lucian Goian met the cross at the near post and accidentally headed the ball into his own net.
With the deadlock broken, the hosts took full control of the midfield and Chennaiyin struggled to string more than a few passes together.
Goa's dream start was made even better when Brandon delivered a terrific cross into the centre of the box from the right-hand side. Mourtada Fall timed his leap to perfection and guided his header past Vishal Kaith and made it 2-0.
The hosts were dominant throughout but were dealt a blow when Boumous picked up an injury midway through the first half. He was replaced by Edu Bedia but the change did not affect the dynamics of the game.
FC Goa started the second half just as they ended the first. Jackichand was at the end of a glorious chance to net Goa's third goal when Seriton's cross from the right flank was cushioned into the path of the Indian winger by Corominas. The former Kerala Blasters forward scuffed his shot from close range and Kaith let out a huge sigh of relief.
The miss soon came back to bite the Gaurs as Chennaiyin scored against the run of play. Rafael Crivellaro received the ball on the left, cut in and unleashed a powerful shot towards the goal. Mohammad Nawaz parried the effort straight into the path of Lallianzuala Chhangte who pushed the ball into the net and stunned the home crowd.
The defence let Goa down again close to the hour mark. Crivellaro sent an inswinging corner into the box and Nerijus Valskis, who was left unmarked, headed in to make it two away goals for Chennaiyin.
Goa nearly turned the game around after the 80th minute. Fall got the ball on the left and his deflected cut-back fell perfectly for Edu Bedia inside the box who slotted into the net.
Two minutes later, the defence failed to clear a long ball into the box and the keeper failed to punch it clear. Fall was alert to the opportunity and headed the loose ball into the net to set up a tense end to the game.
Goa needed two more goals to secure a win but it turned out to be too much to ask for in the last few minutes.