Inviting the faithful to pray at home with family, Damascus announced "the suspension of collective prayer in mosques for Eid," state news agency SANA reported.
The decision by the legal committee of the ministry of religious endowments was aimed at restricting the spread of the new coronavirus.
Damascus has reported 58 cases and three deaths from the COVID-19 respiratory disease in areas of Syria under government control.
Eid al-Fitr is traditionally celebrated by morning prayers in mosques, family visits and large public gatherings.
On May 14, Syrian authorities banned public assemblies during the religious holiday, including at fairs popular with children, and imposed a nighttime curfew from 7.30 pm.
Egypt plans to tighten its curfew during Eid to combat the spread of the virus, as businesses and public transport remain closed.
Al-Azhar, the Sunni Muslim world's leading institution in Cairo, has authorised the suspension of mass prayers at mosques.
Algeria has also ordered specific virus control measures during Eid al-Fitr.