Zamalek must play behind closed doors
The Confederation of African Football's disciplinary committee also fined the club $80,000 and handed them a suspended one-year ban.
Nine people were injured when hundreds of Zamalek fans invaded the pitch near the end of their second round, second leg match against Club Africain of Tunisia in Cairo.
Zamalek were leading 2-1 when the Algerian referee disallowed a headed effort for offside. Had the goal stood it would have ensured the Egyptians progressed to the next round on the away goals rule.
The decision sparked the invasion in which match officials were threatened and several Tunisian players were struck by fans wielding iron rods and sticks.
Egyptian authorities moved quickly to apologise for the incident at one of the first football matches allowed by authorities after street protests toppled president Hosni Mubarak.
Nigerian club Enyimba, also former Champions League winners, were fined $20,000 by CAF and given a final warning for persistent crowd invasions at their ground in Aba.