The Goan club also kept their semi-final hopes alive with a 1-0 victory over Air India in todays another match with Anthony DSouza finding the net in the 85th minute.
Goals from Balwant Singh (21st minute), Eduardo Escobar (50th) and Baldeep Singh (66th) neutralised TFAs early domination, which resulted in a goal from Niroshon Mani in the 19th.
JCT goalkeeper Karanjit Singh missed the line of the ball following P Deepaks throw-in and Mani stabbed home from close to give TFA the lead.
JCTs reply came soon after. Escobar played the ball to an overlapping Jaspal Singh down the right and his cross to the far post was headed in by Balwant. Balwant returned the compliment when he flicked in Daljit Singhs throw-in and Escobar did the rest at the far post. The Brazilian saw one of his efforts rebound off the vertical but JCT did not have to wait long for the insurance goal.
Anwars flick from Escobars corner found Baldeep, who buried his left-footer to the back of the net. TFA showed some spark in the initial minutes with Jagannath Sana testing Karanjit with a long-ranger. But they were no match for the physically superior JCT players.