Ismaily returned to the top of Group B after defeating Masry 2-0 away from home in the Egyptian Premier League on Monday.
Ismaily were level on points with Petrojet ahead of the game, although Petrojet had a better goal difference. Ismaily were lifted by second-half goals from midfielder Ibrahim Hassan and Ghanaian striker John Antwi.
Hassan, who gave Ismaily a precious win with a wonder strike against rivals Zamalek earlier this month, 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, who only drew with Ittihad El-Shorta last week, are now at the top with 13 points from five matches as they host Wadi Degla next week.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)