The defending champions had already earned a 1-1 draw in the first leg, also held at Air Defense Stadium, and advanced with a 3-1 aggregate score.
Mostafa Ziko opened the scoring in the 11th minute, heading in a precise cross from Mohamed El-Chibi on the right flank.
Just four minutes later, Ziko thought he had doubled the lead, but his goal was ruled out for offside. However, replays suggested the striker was onside when the ball was played.
Despite dominating possession, Pyramids FC failed to extend their lead until second-half injury time, when Ethiopian Insurance substitute Birikit Kikaleb scored an own goal to seal the win.
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