The Cameroonian left-back arrowed a superb free kick into the top corner of the net with 14 minutes remaining to settle the contest into Future's favour.
Future were made to sweat for the win even though Bul FC played with 10 men for the majority of the game after Walter Ochora was sent off for a second bookable offence after 20 minutes.
The Egyptian side will face either Buffles du Borgou of Benin or Sierra Leone's Kallon in the second preliminary round for a place in the group stage of Africa's secondary club competition.
Future were expected to secure an easy win following a 0-0 first-leg draw in Uganda but they found it hard to carve out openings in the first half.
They wasted several clear-cut chances after the break though, including a header from defender Saad Samir that struck the crossbar and another from Mostafa El-Badri that narrowly missed the target.
Striker Ahmed Atef also went close with a curling shot before Ngwem eased Future's nerves by breaking the deadlock on 76 minutes.
Future survived a huge scare in stoppage time when the post denied a close-range shot from a Bul FC forward, who was in an offside position although the linesman's flag was not raised.
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