Nepal posted a modest target of 91 runs after losing eight wickets in 20 overs, after Afghanistan elected to field first by winning the toss.
Samiullah Shenwari took 3 wickets in 4 overs by giving only 19 runs, while Izatullah Dawlatzai and Dawlat Zadran took two wickets each.
On the batting side, Nawroz Mangal made a brisk 48 before falling with 11 needed but Gulbadin Naib came in to strike a couple of boundaries, winning the match with a six.
The Afghanistan cricket board chief executive, Dr. Noor Mhammad Murad congratulated the Afghan nation for the victory of the Aghan cricket team in ICC World Twenty20 qualifier semi-final.
The second semi-final is played between Ireland and United Arab Emirates in Abu Dhabi, and the winner of the match will face Afghanistan in the final of ICC World Twenty20 qualifier on Saturday.