This is the first win for the Nepali national team after 11 matches. Nepal also avenged its 1-0 loss against the same team in the SAFF Championship a couple of weeks ago in India.
Nepal's last victory was against India in 2013 at the SAFF Championship held in Kathmandu during which Nepal recorded a 2-1 win.
Since then, Nepal had been winless in 11 matches in a row.
Nepal has sent an U-23 team to Dhaka to prepare the team for the upcoming South Asian Games (SAG) football tournament.
In Wednesday's Group A match, Bimal Gharti Magar's solo goal was enough for Nepal to secure the all important win in the tournament.
Man-of-the-match Bimal put Nepal ahead in the fourth minute slotting in Rabin Shrestha's cross from the Bangladeshi danger zone.
Nepal had created goal-scoring chances in the second half as well, but wasted all the opportunities.
Bikram Lama had chance to double the tally in the 58th minute but his shot off Heman Gurung's free-kick went high above the bar from close range.
With the win, Nepal collected four points from two matches as it had played goalless draw against Malaysia (Felda United) in its first match of the group. Nepal will meet host Bangladesh on Friday at the same venue.
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