The pair were being rehabilitated for the game over the last few days, but today they were omitted from the clash's final squad announced by coach Manuel Jose.
Mercurial Barakat has been suffering from a hamstring problem that kept him out of Ahli's games against Ghazl Mahalla and Kano Pillars.
Skipper Mohamed can't play against Zamalek due to a muscle injury that also forced him to sit out the Pillars' game.
The Red Devils will also have to do without playmaker Hussein Yasser, who is out for the rest of the season with a dislocated shoulder.
While strikers Ahmed Belal and Ahmed Hassan Farag were omitted for technical reasons, substitute keeper Amir Abdul-Hamid will be replaced by Ahmed Adel Abdul-Monem.
However, Jose will be boosted by the return of midfielder Ahmed Hassan and Ahmed Ali from injuries.
Ahli's Squad to face Zamalek:
Goalkeepers: Ahmed Adel Abdul-Monem, Ramzi Saleh.
Defenders: Wael Gomaa, Ahmed Al-Sayed, Mohamed Samir, Ahmed Sedik, Ahmed Ali, Gilberto, Sayed Moawad.
Midfielders: Ahmed Hassan, Hussein Ali, Hossam Ashour, Moataz Eno, Ahmed Fathi, Mohamed Abou-Treika.
Strikers: Flavio Amado, Hani Al-Egeizi, Osama Hosni.