Mustafa Meshaal, who was wounded in the unrest in the port city on Saturday, died of his wounds in hospital on Sunday, medical sources told AFP.
The violence started after an attack on Coptic worshippers in several churches in Alexandria on Friday that left one person dead and several wounded.
Several hundred Copts attended the funeral of 78-year-old Noshi Atta Girgis who was killed by a man using a knife on Friday.
Security sources said 45 people had been arrested following the violence after the funeral. A total of 22 people were injured in the fighting.
The interior ministry said it had arrested Mahmoud Abdul Razik Salah Eddin Hussein, 25, the man suspected of Friday's killing.
Hundreds of Copts attended
Noshi Atta Girgis's funeral
The ministry described him as "mentally unstable".
The official MENA news agency, quoting security sources, said demonstrators "smashed the windscreens of a number of vehicles, burned two other vehicles and some shops", blaming that unrest on "extremist elements".
Witnesses said clashes erupted once again in front of Al-Quidissin church, following prayers marking the Orthodox Church's Palm Sunday.
The church was one of the scenes of Friday's attacks, which were the most serious incidents of sectarian violence since a protest by Muslims accusing an Alexandria church of hosting a play offensive to Islam left three dead in October.
Egypt's Copts - the largest Christian community in the Middle East - account for an estimated 10% of the country's 73 million inhabitants and complain of systematic discrimination and harassment.
Egypt's Copts will mark Easter on April 23.