Banlamkupar Rynjah (27′) and Deibormame Tongper (68′) scored for Meghalaya, with Mohammed Adhnan (90’+1) pulling one back through a penalty kick.
Meghalaya defeated Rajasthan in their opening fixture on 29 April, and Saturday’s second victory puts them on 6 points.
Coach Bobby L Nongbet made just one change to his starting line-up from that match, bringing in Ricky Kharkongor instead of Pyrkhatshaphrang Sumer.
Banlamkupar struck a strong left-footer past a defender and the Kerala goalkeeper from inside the box in the first half to give Meghalaya the lead. Kerala helped with the second goal, with the goalkeeper, Devanandan, failing to clear a back pass. This gave Deibormame the opening to tap the ball into a vacant net.
A foul in the box on the cusp of stoppage time provided some hope for Kerala, but though they converted the spot kick via Adhnan, they were not able to find the equaliser. The Meghalaya boys did well to deny them much possession.
Meghalaya have one more group game to go, against Bihar on Monday.
