Officials say the clashes in the city's el-Dekheila suburb erupted when a Coptic man allegedly sexually harassed a Muslim woman.
Residents of the area fired birdshot and threw Molotov cocktails at one another during the Friday night fighting.
Police say Christian resident Sherif Sedky died of a heart attack during the clashes. Police forces were beefed up around the local church Saturday in case of further violence.
Officials spoke on condition of anonymity because they were not authorised to brief the media.