كتب : Hatem Maher
Ahmed Ali opened the scoring one minute after the restart when he capitalized on Mostafa Fouad's failure to clear the danger to slot home from inside the area.
Former ENPPI midfielder Samir Sabri ensured the victory 11 minutes from time when he converted a penalty after Ahli-target defender Ateya Al-Belkasi felled Sami Abou-Zeid.
Asyut will face Harras Hodoud, who defeated Masri 3-1, in the competition's semis.
Egyptian League surprise package Petrojet will meet ENPPI in the other semi-final tie.
The surprising elimination of the so-called top three - Ahli, Zamalek and Ismaili - gave less fancied teams hope of winning a rare piece of silverware.