The Egyptian international striker Ali struck twice in the first half before Youssef Hamdy added the third early in the second period.
Ali sealed the victory for Cairo giants ten minutes from time while Adel Mostafa scored the consolation for the visitors in the 69th minute.
The second consecutive win under new coach Manuel Cajuda put Zamalek in second place with 32 points while Suez Cement lie in ninth spot on 16 points.
Ali put Zamalek ahead in the 13th minute when he side-stepped a defender inside the area before sending a low shot into the back of the net after being set-up by Gamal Hamza.
The in-form striker doubled the lead five minutes later after meeting a backward header by a teammate with a close-range strike past the helpless keeper.
Hamdy killed off Suez's hopes of returning to the game as he received a brilliant back-heel pass by Hazem Emam before firing a low drive into the bottom corner of the net.
Mostafa scored Suez's only goal in the 69th minute after he fired a powerful long-range shot into the roof of the net.
Ali completed the rout for Zamalek ten minutes before the final whistle when he worked his way through the midfield past Suez catastrophic defense until he went face-to-face with the keeper before slipping the ball home.
Elsewhere, a last-gasp strike by substitute Abdallah Al-Shahat earned Ismaili a hard-fought 2-1 away victory over Masri.
Ahmed Al-Gamal's penalty for Ismaili in the 60th minute cancelled out Mohamed Fadl's opener in the 56th minute before Al-Shahat sealed the victory four minutes from time.
In other matches, Harras Al Hodoud edged Ittihad 1-0, Al-Gaish were held to a 1-1 draw with Koroum and Arab Contractors beat Aluminum 1-0.