The match also witnessed three red cards in stoppage time, with Milan being reduced to nine men as tensions flared
Bhutan exited the tournament after the defeat in the Group A match at Shaheed Rangashala Stadium in Nepal’s Biratnagar on Thursday.
Bangladesh will now face Nepal, who have also reached the semis after Bhutan’s second defeat, next Saturday for the top spot of the group.
After a goalless first half on Thursday, including a cooling break due to excessive hot weather, Mishrat Jahan Mousumi broke the deadlock from a corner kick by Monica Chakma in the beginning of the second half.
Sabina Khatun, who scored six goals in the last edition of the tournament in 2016, extended the lead with a brilliant goal in the 85th minute.
Bangladesh were the runners-up in 2016 and became champions when the tournament was launched in 2010.