Maria Manda shone with an assist and a goal in the match at the Changlimithang Stadium in Thimphu on Monday.
The defending champions, who humiliated Pakistan in their first game with a 14-0 win last week, took the lead against Nepal in the stoppage time of the first half.
Tahura Khatun’s shot from Maria's cross found the net. Maria put the cross from a return pass after taking a short corner shot.
Bangladesh stretched the lead when Maria scored with a long-range shot from outside the box in the 51st minute.
Sajeda Khatun them took the game beyond Nepal's teach with a brilliant goal in the 67th minute.
Nepal had earlier beaten Pakistan 6-0 confirming the berths of their own and Bangladesh in the last four.
Monday’s match only decided their opponents in the semis.
Bangladesh will face Group A runners-up Bhutan on Thursday for a place in the final.
Nepal will play take in India in the other semi-final the same day.
Pakistan and Sri Lanka, who already exited, featured in the tournament for the first time.
Hosts Bangladesh had thumped Neapal 6-0 on way to winning the inaugural championship last year.
The team of Coach Golam Rabbani Chhoton went on to win another four-nation championship held in Hong Kong earlier this year.