Pope Shenouda III of the Coptic Orthodox Church of Alexandria also presided over funerals for some of the Christians killed in Sunday's bloodshed that left at least 26 people dead -- mostly Christian -- and more than 300 injured.
Meanwhile, The New York Times reported Egypt's finance minister Tuesday became the first high-level official to resign since the deadly clashes.
Hazem el-Beblawi had been in office only three months. The official Middle East News Agency reported his departure but gave no explanation, and the Times said he was not immediately available for comment.
The resignation came a day after thousands of Coptic Christian mourners gathered at the country's largest cathedral to commemorate the Christians who were killed. Many mourners harshly criticized the army, which had been praised only eight months earlier for refusing to use force against civilians demanding former President Hosni Mubarak's ouster.
"This is a threat not just to the Copts, but to all of the people. We saw what would happen if we rose up against the army," said Shady el-Ghazaly Harb, a liberal activist.
Witnesses said headless bodies lay in the streets in the worst sectarian violence since the Mubarak's ouster in February.
The Catholic Church in Egypt supported the Copts Monday, accusing Egypt's army and police of using "vagabonds, a rabble force of street fighters, to attack the demonstrators," the Rev. Rafic Greiche, a church spokesman, said in a statement.
The army allegedly hired thugs "were armed with swords, sticks and stones -- some of them had rifles, it seems," he said. "They did not have to use force. It was a peaceful demonstration."
The protesters had said they were attacked by plainclothes "thugs." Then a speeding military vehicle mounted a sidewalk and rammed into a group of protesters, killing a number of them, they said.
The protest spiraled suddenly into a chaotic battle with security forces that started outside the state TV building and soon spread to Tahrir Square, the epicenter of the demonstrations that led to Mubarak's resignation.
Some Muslim and Christian leaders called on followers to put aside their religious differences and focus on what unites them.
"This is more than enough," prominent Islamic preacher Amr Khaled said on Egyptian TV. "We need to remember that Egypt is in danger."