Zamalek were winning 2-1 when the Egyptian side's third goal was ruled out, angering the home fans who took over the pitch and forced the Algerian referee to leave.
It was the second leg of the round of 32 tie. Club Africain beat Zamalek 4-2 in the first leg.
An Egyptian official in the ministry of health said nine people were injured in the incident, according to the state news agency MENA. He did not give their nationalities.
The incident revived the football tension between Egypt and Algeria of the recent past.
Algeria and Egypt had a diplomatic row late in 2009 over an ill-tempered qualification match for the World Cup.
Both sides traded accusations about crowd violence and intimidation and Cairo withdrew its ambassador from Algiers.
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