A penalty conversion by Jaspal Singh helped JCT scrape past New Delhi Heroes 1-0 in a Group C encounter in the 30th Federation Cup at Vidyasagar Krirangan, in Barasat on Monday.
However, their semi-final aspirations evaporated as group leaders East Bengal beat bottom-placed Sporting Clube de Goa.
East Bengal and JCT had six points prior to the former's match and even a draw would have ensured the red-and-golds passage to the last four stage.
Sukhwinder Singh's boys missed as many as three sitters and needed a 15-minute penalty to ensure full points.
New Delhi Heroes midfielder Barrister Rymbat handled the ball inside the box and the referee had no hesitation to point to the spot.
JCT's hopes of increasing the tally were blown away by strikers Balwant Singh and Balraj Singh.
Sukhwinder, who was hoping for a better strike rate was disappointed with the outcome.
"Players lacked force. We almost missed three-four sitters which would have definitely given us an edge to qualify for the semi-finals. Now, it's very difficult," said the JCT coach.