The Shillong side continued their fine form in the second tier of the competition and sealed the lone berth available in the nation's premier tournament.
While a draw would have been enough for Bhawanipore to go through, only a win in the duel would give Wahingdoh a place in the country's top division.
With coach Juliano Fontana suspended for involving himself in a brawl in one of the previous matches, Jose Ramirez Barreto, the veteran striker had extra responsibility as he gave occasional advice to the team that started with a 4-4-2 formation with the pair of Daniel Bidemi and Dipendu Dowary operating upfront.
On the other hand, it was Badmus Babatunde, the former ONGC and Rangdajied United striker who was leading the charge for the Shillong side alongwith Jackichand Singh.
Daniel Bidemi, the prolific Nigerian striker of the Kolkata side handed his side the lead in the 23rd minute after finishing perfectly following a good build-up by his team.
After conceding the goal, Wahingdoh showed commendable alacrity and invaded the Bhawanipore box a couple of times after the half-hour mark. In the 37th minute, Jakichand scored the important equaliser as he pulled the trigger from outside the 18-yard territory to restore parity for his side.
After the break, Babatunde had put his side into the lead as his powerful shot gave Debjit Majumder little chance to react between the sticks.
Daniel Bidemi scored once again in the 74th minute to give Bhawanipore the advantage when he timed a header perfectly from a Gurpreet free-kick to pull one back.
However, Bekay Bawar, the Liberian member of Wahingdoh squad scored the most important goal of the fixture as he calmly placed the ball into the net taking advantage of a quality build-up from his side.
With this, Wahingdoh becomes the third Shillong side to be part of the nation's most prestigious league tournament, given Rangdajied United avoid the drop and fulfill the club licensing criteria.