State television broadcast images of the president entering the Hassiba mosque and waving to the supporters before taking part in prayers.
The prayers were led by Imam Mohamed Tawfik al-Bouti, the son of Mohamed al-Bouti, a senior pro-regime religious figure who was killed in a bombing at a mosque in March.
Assad, who has rarely been seen in public since the beginning of the conflict in Syria, attended prayers at a Damascus mosque on August 8, for the Eid al-Fitr holiday.
More than 115,000 people have been killed in Syria since the beginning of the conflict in March 2011, according to the Britain-based monitoring group.
