A Cornell Glenn hattrick (16th, 53rd and 91st minute) along with a Boithang Haokip (24th) strike handed Mumbai FC their biggest defeat in this season's group stage.
The loss also meant that Mumbai FC ended their Fed Cup campaign winless and finished at the bottom of Group C.
The game began with Mumbai FC almost taking the lead in the opening exchanges. After medio Climax Lawrence set up Henry Ezeh, the striker went past defender Wailad Passah only to see his attempt come off the woodwork.
Haokip then doubled the lead after finishing off Robin Gurung's pass midway through the half.
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Mumbai FC had a few half chances but failed to make them count as they went into the breather trailing 0-2.
Mumbai FC went close once again eight minutes into the second half through Ghanaian striker Yusif Yakubu who was denied by goalkeeper Vinay Singh from close. However, Shillong increased their lead on the resultant counter attack.
Mumbai FC tried to push ahead in the final exchanges of the game, but were constantly denied by the Shillong 'keeper.
Into injury time, Glenn completed his hattrick with a well taken freekick.