Coach Hassan Shehata reverted to a traditional 3-5-2 formation after the 4-4-2 strategy let him down in Egypt's opening 1-1 draw at home to Sierra Leone.
Fathallah has been playing as a central defender since joining Zamalek from Ghazl Mahalla in 2007.
The 28-year-old's club teammate Hani Saied was expected to play as a sweeper, a position he occupied in Egypt's triumphant Nations Cup campaigns in 2008 and 2010, but Shehata suddenly put him on the bench.
Ahli's evergreen defender Wael Gomaa partners Sherif Abdul-Fadil, who is given a rare start, in the heart of Egypt's backline.
Ahmed Fathi, who usually plays as a right-back at Ahli, returned to his favorite position in central midfield. He will be accompanied by his club teammate Hossam Ghaly.
Amr Zaki returned to the starting line up after missing the Sierra Leone game due to disciplinary problems. He will partner Ismaili's Ahmed Ali upfront.
Egypt line up:
Goalkeeper: Essam Al-Hadari
Defenders: Mahmoud Fathallah, Wael Gomaa, Sherif Abdul-Fadil
Midfielders: Ahmed Elmohamady, Ahmed Fathi, Hossam Ghaly, Mohamed Abdul-Shafi, Mohamed Abou-Treika
Strikers: Amr Zaki, Ahmed Ali