Local team Zamalek were leading Tunisian visitors Club Africain 2-1 as the second round, second leg qualifier drew to a close and needed another goal to squeeze through on the away-goal rule, having lost 4-2 in Tunis two weeks ago.
The five-time African champions thought they had gotten that goal when an Ahmed Gaafar header landed in the net, only for the Egyptian to be ruled offside by the Algerian match officials, with television replays backing the decision.
This sparked a pitch invasion, initially, by a few Zamalek fans, but soon followed by several hundred. Track-suited security officials successfully raced in to protect the referee and his assistants before escorting them from the field.
African Champions League organisers seem likely to award the tie to Club Africain while Zamalek could face a variety of punishments, including a fine and being forced to stage African fixtures outside Cairo and behind closed doors, locking fans out.
Egypt had hoped to resume the 16-club national championship on 15 April after a three-month stoppage caused by the revolt that ousted long-time authoritarian ruler, Hosni Mubarak.
However, national football association president Samir Zaher announced that the decision would have to be reconsidered after what happened at the 75,000-seat Cairo Stadium late Saturday.
"This is not promising ... what happened makes us reconsider. What will happen if we resumed the league [matches] and the fans of two bitter rivals, such as Ahly and Zamalek, are at the same stadium?" asked Zaher.
Prime Minister Essam Sharaf ordered the interior ministry to launch an investigation and called for a suspension of the domestic competitions, describing Saturday night's incident as "an act of thuggery." Furthermore, he will not allow these acts to go unpunished.
This was the fifth African club fixture to be staged in Egypt since Mubarak lost a three-decade grip on power and the first at which there were crowd incidents.
The other four matches went without incident because they lacked the appeal and passion that comes with a clash between teams from North African countries, especially when the fierce rivalry that has developed in regional and Pan-African competitions rises to the surface.