The Cairo giants, leading 2-1, were on the verge of exiting the competition from the preliminary round after failing to overturn a 4-2 first-leg deficit.
Zamalek had a goal disallowed for offside and few minutes later thousands of fans stormed the pitch as security personnel rushed to protect the referee and the linesmen.
The ugly scenes saw angry hooligans throw stones and damage the goal�s posts in unprecedented disarray in Egyptian football. Reports at Cairo Stadium said some players were injured amid the chaos.
African are expected to be awarded victory and Zamalek is likely to face sanctions from the Confederation of African Football (CAF).
The Egyptian Premier League was scheduled to resume 15 April but the incident could throw that into doubt.
Watch the fans breakout in Cairo Stadium
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Video: 2
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Ahmed Shobier talks about the event
Watch the Goals of the match here (Click here)
Club African Manager speaks about the game:
Mido Speaks about the Event: