Salgaocar's Isfaq Ahmed cancelled the first-half strike by Amer Abdel Abuhwaiti.
Mahmoud Shelbaieh who scored in all the three matches earlier, struck the winner in the 82nd minute.
Salgaocar remained on one point from four matches and are out of contention for the knockout stage.
Salgaocar, in the absence of their three foreign players, put up a defencive approach and the visitors who started cautiously played at a slow pace and kept the ball within themselves after taking the lead in the eighth minute, which frustrated the crowd.
The visitors took the lead from a swift move on the right by Mahmoud Shelbaieh who released the ball to Abuhwaiti who took two rival defenders in his stride and beat onrushing keeper Karanjit Singh.
Salgaocar who put up a better performance in the second half, received a setback when defender Ibrurbam Meitei was sent off by referee Uda Jumpei for receiving his second card for a dangerous foul on Issa Alsapah in the 57th minutes. A few minutes later striker Balwant Singh limped out. PTI MCS ABC AH