In what was one of the deadliest attacks on the religious minority in recent memory a bomb exploded during Sunday Mass at a chapel adjacent to St Mark's Cathedral in the capital.
The coffins of the 24 victims were laid in front of the altar on Monday, with the names of each one displayed on the side facing the congregation.
Relatives screamed in grief, sobbed or sat in silence as the leader of the Coptic Orthodox Church led the prayers.
At one point, the visibly distraught pontiff leaned on his staff and quietly prayed in front of the coffins. He had cut short a visit to Greece and flew home on Sunday after the bombing.
"God, protect us and your people from the conspiracies of the evil ones," prayed the Coptic pope - who venerated the coffins with incense.
In a sermon, he said: "It is the destiny of our church to offer martyrs and that is why we call it the Church of the Martyrs."
"We are in so much pain over the evil that surrendered all the humanity and feelings that God entrusted in man," said Pope Tawadros.
"Those who take a life, which is a divine gift, will be granted eternal damnation."
He revealed that he had taken a call from Pope Francis in the aftermath of the atrocity.
Egypt's president blamed a suicide bomber for the explosion. Abdel-Fattah el-Sissi identified the bomber as 22-year-old Mahmoud Shafiq Mohammed Mustafa.
He said three men and a woman have been arrested in connection with the attack.
The president spoke after Health Ministry officials revised down the number of victims to 24, suggesting that the 25th body belonged to the bomber.
After the prayers the coffins were carried out of the church and loaded onto ambulances that would take them to a parade ground in Nasr City, where a separate state funeral was due to be held later.
President Abdel-Fattah el-Sissi, who declared a three-day state of mourning following the attack, will attend the funeral.
Some women passed out as the coffins were taken out of the church. Others called out the names of the victims in anguished screams.
Bishop Angaelos, General Bishop of the Coptic Orthodox Church in the UK, said: "Today is a day of many emotions: sadness, nervousness, uncertainty, and understandably even anger at times.
"That is because yesterday was a day in which we witnessed the worst of humanity, when innocent women and children who decided to worship their God in their spiritual home had their lives needlessly and senselessly ended without warning.
"They were used as pawns; a means to an end. To the perpetrators of this heinous crime, their lives clearly held no greater value than scribbles on a strategic page; a plan that was to be executed for a cause to which they were merely incidental, collateral damage."
