The victory was their first in the ongoing I-League 2013-14.
Second half goals by striker Orok Essien (46th minute) and midfielder Climax Lawrence (87th) completed an impressive 2-0 score-line over the defending champions in a Round-3 encounter at the Duler Stadium.
The win helped Mumbai FC jump from sixth spot into second behind United SC.
Overall this was the second time ever that Mumbai FC had beaten the Goans in 11 meetings. The other win (2-1) was logged in a home game at the Balewadi Sports Complex.
Similarly, Valeriano Rebello's timely clearance to deny rival striker Henry and a solid performance by Haroon Amiri, Kamaljeet Kumar and debutant Sandjar Ahmadi led to Mumbai FC's success.
Into injury time, Mumbai FC's Valeriano ensured his team walked out with a clean sheet thwarting a certain goal by Henry who chased a long ball, got in the clear and managed to tap over the onrushing Kunal.