In a match between last edition finalists, which was also their respective final matches this season, Goa prevailed over the Chennai side with 21-year-old Tavora firing in a screamer from the edge of the box into the Chennaiyin goal with just a few seconds left in the three-minute injury added time to end a dramatic match.
Coming as substitute at the start of the second half, Tavora had scored his first goal of the match in the 68th minute. Goa's other goals came from Rafael Coelho (6th and 76th) and Joffre Gonzalez (21st).
Goa, coached by legendary Brazillian footballer Zico, ended their campaign on a high but they still finished at the bottom of the league table with 14 points from 14 matches (4 wins, 2 draws, 8 losses).
In a way, they avenged last year's controversial summit clash at the same venue, where Zico's side ended as runners-up with Chennaiyin lifting the trophy.
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Chennaiyin, coached by Italian World Cup winner Marco Materazzi, ended just one place above Goa at seventh place with 15 points from 14 matches (3 wins, 6 draws, 5 losses).
18-year-old Jerry Lalrinzuala of Chennaiyin also became the youngest scorer in ISL 3 when he curled in a brilliant free-kick into Goa net in the fourth minute of the match.
A move from the middle saw Richarlyson Felisbino foul on Anrirudh Thapa just outside the box and Lalrinzuala sent the ball to the far corner of the net giving keeper Laxmikant Kattimani no chance to react.
The visitors once again took the lead in the14th minute. Thoi Singh made a run into the box from the right, took a crack at the goal which keeper Kattimani blocked but the ball fell on the path of Anirudh Thapa whose shot deflected defender Gregory Arnolin and went in.