Tensions flared, gunfire broke out and the two sides threw firebombs and stones. Soldiers and police rushed to the church, fired shots in the air and used teargas to separate them, the witnesses said.
A Reuters witness said later that another church in the same area was on fire and had been severely damaged.
State media gave the new death toll and revised the number of injured to 186, with two in a critical condition in hospital. At least five were reported dead late on Saturday and 75 injured.
One of the new corpses was found inside the church, official news agency MENA reported.
It was some of Egypt's worst sectarian violence since January and offers a new test for the generals who took power after the overthrow of Hosni Mubarak in a popular uprising.
Police who deserted the streets during the uprising have returned to their jobs, but many Egyptians say they feel less safe on the streets.
Prime Minister Essam Sharaf cancelled a tour of Gulf States to call an emergency cabinet meeting on Sunday morning to discuss the violence, MENA said.
Sectarian strife often flares in Egypt over conversions, family disputes and the construction of churches. Muslims and Christians made demonstrations of unity during the protests that overthrew Mubarak, but interfaith tensions have grown.
Christians make up about 10 percent of Egypt's 80 million population.