Published : 22 Jan 2016, 07:33 PM
Bimal Gharti Magar, Bishal Rai and Nawayug Shrestha were on target in the final at the Bangabandhu National Stadium on Friday.
Nepal won their last title in 1993, beating India in the final of the Asian Games.
Bahrain were represented by their national Under-23 team.
The South Asian team took an early lead when Bahrain goalkeeper Mahboob Aldoseri failed to clear an Anjan Bista header. It allowed Bimal to find the back of the net from close range in the fifth minute.
Both teams picked up pace in the second-half but squandered a number of chances.
As the intensity rose, Bahrain midfielder Ahmed Althuani and Nepal forward Sumon Lama were caught in a physical struggle. The referee took control by giving marching orders to both the players.
Bishal then extended Nepal's lead with a flick past the goalkeeper to all but seal the win. But Shrestha added another in the dying seconds of the match with a fine header.