During an emergency assembly of the Egyptian parliament on Thursday morning, the decision was taken to dismiss the association's president and all of his staff
The violence broke out when thousands of Al-Masry supporters streamed onto the pitch shortly after the full-time whistle to attack Al-Ahly players and fans, resulting in the deaths of at least 73 people.
An emergency meeting was called by the Egyptian parliament for Thursday morning, during which Al-Ganzouri announced the dismissal of Zaher and his entire staff.
Al-Ganzouri also revealed that the governor of Port Said province and the area's police chief have both resigned from their respective positions.
However, Zaher plans to challenge the Egyptian PM's decision on the grounds that government interference in footballing matters is not prohibited by Fifa, meaning there is now a chance that Egypt will be prevented from competing in this summer's Olympic Games.
According to the Associated Press, there have been accusations from eyewitnesses that the riot police present at the ground made no attempt to stop Al-Masry fans as they moved to invade the pitch.
That view was backed up by Al-Ahly midfielder Mohamed Aboutrika, who claimed: "The security forces left us. They did not protect us. A fan just died in the dressing room in front of me."
Al-Ahly coach Manuel Jose has sought to have his contract terminated during a meeting with club president Hassan Hamdi, while players Mohamed Barakat and Emad Meteb have vowed never to play for the team again.
The Egyptian FA's final act before dissolution was to indefinitely suspend the Premier League.