State television showed footage of Assad and his wife Asma making the visit overnight to the Notre Dame de Damas Church, where he was shown chatting to the choir.
He took a seat near the altar and listened to a recital of Christmas poems in the main cathedral hall, Reuters reported.
The surroundings of the church in the old part of the ancient capital were hit by mortar fire on Friday, officials said.
The church is only 2 km away from Jobar, a neighborhood of the rebel-held eastern Ghouta suburb of Damascus that has been the focus for months of heavy aerial bombardments.