Kshitiz Raj GT scored the winner in the second half of the evenly contested game played at the water-logged Sylhet District Stadium, Bangladesh, where rain delayed the start of the play by half-an-hour.
The win also helped Nepal remain unbeaten in the championship as it reached the last four having defeated the Maldives 5-0 in the opener on Monday.
Despite the defeat, Afghanistan also entered the semifinals as Group B runner-up as it had thrashed the Maldives 4-2 in its previous match. The Afghans next face Group A winner Bangladesh in the semifinal on Sunday.
Nepal, the runner-up of the last edition, will now face defending champion and Group A runner-up India in the other semifinal on Sunday.
India had defeated Nepal 1-0 in the final to claim the title of the second edition played at the Dasharath Stadium in Kathmandu in 2013.
On Friday, the first half of the game ended 0-0 as Nepal missed a solid chance of taking the lead in the hardly playable condition of the ground.
Prezan Tamang's shot went inches wide of the Afghanistan post in the 35th minute.
However, Nepal finally broke the deadlock within three minutes after the break.
Kshitiz Raj helped Nepal lead 1-0 in the 48th minute. After that, both the teams failed to add any more goal and Nepal held on to victory.
PHOTOS: ANFA
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