Mohamed Samir played as a sweeper behind two central defenders in Wael Gomaa and Sherif Abdul-Fadil.
Youngster Ayman Ashraf, deputizing for the injured Sayed Moawad, played on the left while Egypt's versatile midfielder Ahmed Fathi retained his place on the right flank.
Striker Mohamed Fadl made his comeback after recovering from a knee injury he picked up last month as he was introduced in the second half.
Classy playmaker Mohamed Abou-Treika, who looked way past his best under former coach Hossam Al-Badri, opened the scoring 10 minutes after the break following a neat exchange of passes with Abdul-Hamid Shabana.
Midfielder Moataz Eno wrapped up the victory late in the game with a fierce drive that went in off the post.
"The players will need time to adapt to the formation we use now," Zizo, who took over at Ahli on a temporary basis, said.
"Samir played well as a sweeper, he followed all the instructions," the Ahli great, who face a dilemma over who can fill that role, added.
Zizo will make his competitive debut at the helm when Ahli face promoted Smouha in the Egyptian Premier League on Thursday.
The defending champions, who eye a seventh consecutive league title, lie fifth in the table with 18 points from nine games, six behind leaders and arch rivals Zamalek who played two matches more.