Douhou Pierre, the Ivory Coast striker, scored a brace, while Clifton Dias and Zambian defender Francis Kasonde netted the other two goals for the victorious Goan side in a Group B match at the Tilak Maidan.
Mohun Bagan have two points after three matches while Salgaocar have six points from three matches.
Mohun Bagan started the match brightly with Cameroonian striker Pierre Boya giving the green-and-maroons lead early in the 28th minute.
They enjoyed possession in the midfield and created chances but lacked proper finishing. But Boya managed to rectify that, turning with a superb first touch and gently toe-poking the ball into the back of the net past an onrushing Salgaocar goalkeeper Subrata Pal.
Salgaocar equalised quickly. Midfielder Saran Singh forced his way after exchanging passes with Pierre and then managed to feed the latter who showed great composure and curled the ball into the net on 35 minutes.
Salgaocar threatened to take the lead just at the stroke of half-time but Scottish striker Darryl Duffy wasted a glorious opportunity, blasting his shot wide from close range.
After the breather, Salgaocar slowly stepped up the pressure and controlled the mid-field.
Mohun Bagan goalkeeper Shilton Paul saved his team from concedeing on several occasions, palming away a shot from Pierre.
But he couldn’t keep out Kasonde’s rebound shot at the 75th minute after blocking a Francis Fernandes header.
Piere then inflicted more misery on Mohun Bagan as he dribbled past two defender to score in the 90th minute.
Dias completed Mohun Bagan’s humiliation a minute later, scoring from a shot from just outside the box, which trickled over the goal line after hitting the outstretched left hand of Paul.