Jaison Vales and Bikash Jairu found the target from rebounds in the first half and Rocus Lamare scored from a penalty. Mumbai FC got their lone goal through Milagres Gonsalves late in the match.
The defeat ended the Mumbai club's six games unbeaten run. Mumbai FC with 12 points have moved a rung down to 7th position in the 11-team table. Salgaocar, who were beaten 3-0 by the Mumbai side in the away match, tally 14 points and have climbed to the 4th position.
Mumbai FC took that setback in their stride and fought on gamely. They created a couple of chances and in the 18th minute Bheke with a measured cross found ace striker Josimar Da Silva unmarked in the centre. But Josimar's header was collected by Salgaocar goalkeeper Subrata Paul to deny Mumbai FC the equaliser.
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The Khalid Jamil coached Mumbai FC outfit went all out in search of goals in the second period and came close in the 59th minute. But Mohammed Rafi's snap attempt had goalkeeper Paul completely beaten and the ball struck the upright, much to the dismay of the Mumbai FC players.
Mumbai FC finally found the net in the third minute of injury time as substitute Gonsalves dived in at the far post to nod home Rafi's cross from the left.