Appearing in public for the first time since a rare speech on January 6, Assad was shown in a live television broadcast, flanked by Syria's Grand Mufti Ahmad Hassoun and the religious endowments minister.
After the brief ceremony in Al-Afram mosque attended by dozens of religious clerics and laymen, the president smiled and seemed at ease as a crowd gathered to offer greetings.
Religious Endowments Minister Mohammed Abdel Settar earlier called for "million man prayers" at mosques on Friday to appeal for the re-establishment of security in the country, rocked by a deadly unrest for the past 22 months.
"Prayers will be held after Friday services in Syria's mosques with the appeal for a return to security and safety in the homeland," Abdel Settar said
Syria has been experiencing unrest since mid-March 2011. Many people, including large numbers of security personnel, have been killed in the violence.
According to a UN report, extremist militants from nearly 30 countries have been filtered into Syria to fight against the government.