Phrangki Buam was the scorer of Meghalaya’s lone goal.
Railways didn’t turn up for the tournament, so Meghalaya’s first match took place on Wednesday against Nagaland, which ended 6-1 in Meghalaya’s favour.
Manipur, meanwhile, had drawn 0-0 with Nagaland on Monday.
The Meghalaya team will now return home. The final round will begin at a date to be announced by the All India Football Federation.