It was the worst violence since the downfall of President Hosni Mubarak last month.
Six Christians and five Muslims were shot dead, security sources told The New York Times, and about 100 people were wounded.
"The army prevented us from entering," said Adel Azouz of the Cairo ambulance service. "The people who fought each other might have thought that our ambulances were there to offer support to the other side."
Father Abdelmaseeh Baseet of the Coptic Church told CNN the fighting broke out after Copts protested last week's burning of a church in Helwan province.
The Helwan church burning reportedly stemmed from an inter-religious romance and family feud.
Opposition figure George Ishaq appealed for an end to the violence and told al-Jazeera those fighting were "the real enemies of the revolution" and may have been agents of Mubarak's party and state security.
Tensions between Christians and Egypt's Muslim majority have been high in recent months.
On New Year's Day 23 people were killed in the bombing of a church in Alexandria, the capital of Coptic Christianity.