The win secured the Red Devils a FIFA Club World Cup Qatar 2020 semi-final against European giants Bayern Munich.
The hosts started brightly, but the African champions got into their rhythm after ten minutes and began to dominate.
Their reward came on the half-hour, when Walter Bwalya pressured Bassam Hisham into a defensive mistake.
The ball broke to Hussein Elshahat, who arrowed a low drive into the bottom corner from just outside the penalty area for Al Ahly.
Bwalya thought he had doubled the lead shortly later after he broke the offside trap, but his effort was ruled out for offside.
Al Duhail threatened to equalise just after the hour. Edmilson Junior broke free down the left and fizzed in a cross.
Michael Olunga did well to react to it, but Mohamed Elshenawy’s handling was up to the task.
The Qatari outfit continued to probe for an equaliser, but the Egyptians held on for victory.
Al Ahly will now face Bayern at Ahmad Bin Ali Stadium on 8 February.