In the 67th minute, Deepak Mandal of JCT stunned Air-India with a kick from half-line which sent the ball sailing over the rival defenders, including goalkeeper Partha Das, to land in the net.
Ten minutes later, Hardip Sangha from the left flank scored off an angled shot to complete the tally.
With this victory, JCT have accumulated 16 points from nine matches, boosting their chances to qualify for the Super League stage.