Despite beating Chirag United 1-0 in their season-ending match on Friday, Sporting Clube de Goa finished 13th in the standings and could not avoid relegation to the second division.
Substitute Anthony D'Souza scored the winning goal in the 66th minute in the last-round match of the league at Howrah stadium as the Kolkata outfit paled in comparison to the Goan side.
But the win was of little consequence to Sporting as Mumbai FC shocked last year's runners-up Mohun Bagan 2-0 in a home match to remain unscathed.
The result was heartbreak for the Goan side, coached by Vishwas Gaonkar.
It was an irony of sorts for Sporting as their under-19 boys are fighting for the title against East Bengal on Sunday in the tournament for I-League teams.
Chirag United seemed out of sorts in the first-half, even as Sporting squandered many chances to go ahead.
Sporting finished with 27 points and placed second last as Lajong FC emerged the wooden-spooners with 26 points.
Mumbai FC avoid relegation
Riding on skipper Abhishek Yadav's twin strikes, Mumbai FC defeated Mohun Bagan 2-0 and avoided the relegation.
Yadav scored in the 11th and the 24th minute as Mumbai FC, who desperately needed a win to stay in the elite division of the I-League, repeated their 2-0 victory over the Kolkata giants in their earlier group match.
With this win, Mumbai FC have 29 points from 26 matches and moved to the 11th place in the league table, displacing city club Air India, who also survived the drop despite a 5-1 thrashing at the hands of Churchill Brothers.
Sporting Club de Goa, who defeated Chirag United and Lajong FC, have been eliminated and will be replaced by local club ONGC and Bangalore's HAL.