President Abdel Fattah al-Sisi the day before named the suicide bomber as Mahmoud Shafik Mohamed Mostafa, 22
Magy Magdy died at dawn from shrapnel wounds to the head following the suicide bombing on December 11 that was claimed by the Islamic State (IS) group, it said in a statement.
The bombing during mass at the Saint Peter and Saint Paul church was the deadliest attack in recent memory to target Egypt's minority Coptic Christians.
Seventeen people remain in hospital including three in serious condition, the ministry said.
Previous death tolls for the bombing included the attacker.
On December 13, IS identified the suicide bomber by the pseudonym Abu Abdallah al-Masri.
President Abdel Fattah al-Sisi the day before named the suicide bomber as Mahmoud Shafik Mohamed Mostafa, 22, during a funeral for the victims.
Egyptian authorities are battling an Islamist insurgency, mostly in North Sinai province. Some attacks have targeted security forces and officials in Cairo.
The attacks have worsened since the July 2013 ouster of Islamist president Mohamed Morsi, which was led by then army chief Sisi.
This month's blast was the worst attack on the Coptic Christian community since a 2011 suicide bombing killed more than 20 worshippers outside a church in the coastal city of Alexandria.