Ghanaian striker John Antwi scored to help Ismaily return to the top of Group B after defeating Masry 2-0 away in the Egyptian Premier League on Monday.
Ibrahim Hassan broke the deadlock two minutes after the interval when he pounced on a loose ball to slot home the opener.
League top-scorer Antwi then doubled his side's advantage with a left-footed strike in the 79th minute for his fifth goal of the season.
Ismaily were level on points with Petrojet ahead of the game, although Petrojet had a better goal difference.
They are now at the top with 13 points from five matches as they host Wadi Degla next week.