Palestinian striker Oday Dabbagh opened the scoring in the 21st minute, while defender Hossam Abdel-Maguid converted a penalty six minutes before halftime.
Despite the victory, Zamalek remained fourth in the standings on 25 points, seven behind leaders Ceramica Cleopatra, who have played one game more.
Petrojet began brightly and pressed a struggling Zamalek side — which fielded several youth and fringe players — during the opening 10 minutes, but failed to create any clear-cut chances.
Zamalek capitalized on that wastefulness when Nasser Mansi released Dabbagh on a counter-attack.
His initial effort was saved by the goalkeeper, but the striker followed up to score from the rebound into an empty net.
Dabbagh later won a penalty, which Abdel-Maguid calmly dispatched, sending the goalkeeper the wrong way.
Zamalek nearly added a spectacular third just before the break when Adam Kaied’s scorpion kick struck the woodwork.
The second half was largely uneventful, with Petrojet struggling to break down a Zamalek side content to protect their two-goal lead.
The visitors’ best chance came in the 69th minute when substitute Gabriel Chukwudi missed from close range.
At the other end, Brazilian winger Juan Alvina and a Tunisian striker — both introduced after the break — squandered one-on-one opportunities, with Petrojet goalkeeper Omar Salah denying them twice.
Zamalek next face fellow Egyptian side Al Masry in a Confederation Cup group-stage match on Sunday.
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