Meghalaya's goals were scored by Dibinroy Nongspung (8th minute) and Bisharalng Kharumnuid (76th).
With Goa splitting points against Chandigarh today, West Bengal, who have seven points, are through to the semi-finals from Group A.
The second place from Group A will be decided between Goa, Services and Meghalaya when they play their last matches.
Meghalaya, who opened their account with today's win, have a chance to qualify for the semi-finals, having garnered three points from as many matches.
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Hardworking Enestar Malngaing's cross from the left flank found Dibinroy Nongspung inside the box. He controlled the ball before essaying a stiff grounder to find the far corner of the net.
Stung by the reverse, Services mounted pressure on the rival citadel with repeated forays but failed to find the equaliser on three occasions.
In the last quarter of the first half, Services were all over the rival in search of the equaliser but Britto PM's header from close range went just wide.
Services continued in the same way after the break but goals continued to elude them.
Meghalaya, who were seen defending their citadel, came with counter moves and increased the lead in the 76th minute.
(REOPENS SPD 22)
Meanwhile in another final round Group A league match of the Santosh Trophy, Goa missed a number of chances to settle for a 1-1 draw against Chandigarh at Athletic Stadium in Bambolim.
Services and Megahalaya, who have three points each, now need to win their last match along with Goa in order to qualify for the semi-finals as the second team from this group.
West Bengal, who have seven points and a game in hand, are leading the table and are the first team to qualify for the semi-finals.
Goa got off to the perfect start when Aaren D'Silva tapped in a Francis Fernandes cross from inside the box to give the hosts the lead in the 13th minute.