Two men have been arrested over the attacks on mourners at Abbasiya Cathedral on Sunday.
The suspects, aged 17 and 21, were arrested on Monday night and are still being questioned, state news agency MENA reported.
Violence erupted on Sunday when unknown assailants attacked mourners as they exited the cathedral after a funeral for Copts killed in sectarian clashes in Qalioubiya, north of Cairo, in the early hours of Saturday.
As Sunday's violence escalated, plain clothes men threw rocks and Molotov cocktails at the cathedral, while police fired teargas and birdshot directly into the cathedral compound. Two people died in the violence.
A health ministry official said at least 90 people, including 11 policemen, were injured.