Sangti Janai Shianglong (40th) reduced the margin to 2-1 in the first-half but there was more drama in store as Meghalaya made it three-all with a second-half brace by Shano Tariang (46th, 65th).
Four minutes later, a long ball found Dilip Orawn in space down the right as his pinpoint cross was met first time by Mahitosh Roy and he swept the ball home to seal three points for Bengal.
Bengal goalkeeper Priyant Singh also made an incredible double save to thwart Meghalaya's efforts in the dying minutes.
Bengal now have six points from three matches, one point shy of leaders Kerala, who are unbeaten from three matches in group A.
Bengal will face Rajasthan in their last group A fixture on Sunday.
Bengal completely dominated the first-half and used their flanks to great effect.
Fardin Ali Molla and Dilip Orawn were live-wires throughout the opening period.
A few long range attempts were tried by the Bengal players before the first goal of the game.
The 20-year-old took his shot first-time and the ball rifled into the net with the goalkeeper remaining a mere spectator.
Things quickly changed in the 40th minute when Subhankar Adhikari made a hash of an easy clearance from an innocuous through ball attempt.
Sangti Janai Shianglong punished the mistake and Meghalaya restored parity against the run of play.
It took two minutes for Bengal to restore their one-goal advantage when Molla converted a penalty.
In an action-packed second half, Shianglong was clean through on goal and he made no mistake, slotting the ball home past a diving Priyant Kumar Singh.
Roy made up for his numerous misses in the 49th minute with a fierce overhead kick to make it 3-2 in Bengal's favour.
Once again, the Bengal lead did not last long and Meghalaya took advantage of another defensive howler, this time from skipper Monotosh Chakladar.
Kynsaibor found himself free on the right and his cross was turned in by substitute Shano Tariang.
A hat-trick of errors led to easy goals for the team from the North-East.
Meghalaya kept pressing more and more but only to give away too much space for the counter.
And in the 69th minute, one such move paid dividends for Bengal when a long ball found Orawn in space down the right.
His pin-point cross was met first time by Roy and he swept the ball home to seal the issue.