Salgaocar scored through Bikash Jairu (58th) and Gurinder Kumar (64th).
Shillong Lajong, who were at the receiving end for most part of the match, scored a consolation goal in the injury time through Jacob Lalrawngbawla (90+3).
Salgaocar, who lost their first match against Bengaluru FC, have three points from today's win. Shillong Lajong, who suffered their second defeat, are yet to open their account.
Salgaocar started promisingly as they looked for an early goal but the rival keeper came out with some good saves to deny Pierre and Duffy early success.
More From This Section
However, the best chance for Salgaocar came midway in the first half but Gilbert Oliveira, who was unmarked inside the rival box, shot wide off the target after he was fed by Jairu.
Salgaocar kept on moving the ball from the flanks and Bikash Jairu, who was denied by the rival keeper twice in the first half, finally scored after the change of ends as he beat an off side trap and met a Duffy through pass in the 58th minute.
Lajong, who looked listless in the first half, had a couple of chances. But Subrata made a diving save from a Samuel Shadap shot and then a Dungel feeble shot off Jacob Lalrawngbawla did not trouble the keeper in any way.
Lajong scored a consolation goal in the injury time as Jacob Lalrawngbawla's effort from the right took a deflection off defender Kasunde before landing into the net.