Complying with stringent social distancing rules, worshippers kept a minimum of two metres apart.
They had been instructed to bring their own prayer mats and to perform the cleansing ritual, or ablution, at home, instead of in mosque grounds.
"Worshippers rushed to the home of God to perform their obligatory duty [prayers]after the reopening of mosques," the Ministry of Islamic affairs said on Twitter.
The ministry posted a video showing a mosque with many worshippers wearing face masks and reaching out for a large bottle of hand sanitiser after prayers.
Authorities have instructed mosques to avoid crowding and the distribution of food, drinks, incense and miswak twigs used to clean teeth, according to the ministry.
Easing curbs
Saudi Arabia, home to Islam's holiest sites, had shut down mosques nationwide for more than two months to limit the spread of the COVID-19 respiratory disease.
The kingdom, which has reported the highest number of coronavirus cases in the Gulf, is emerging from a full nationwide curfew imposed during Eid Al Fitr, the Muslim holiday that marks the end of the fasting month of Ramadan.
Domestic air traffic also resumed on Sunday, with state media saying around 100 flights were scheduled.
The interior ministry intends to ease restrictions in a phased manner, with the curfew lifted nationwide –- except in Mecca -- between 6:00am and 8:00pm (03:00 GMT and 17:00 GMT) until June 20.
The kingdom will lift the lockdown entirely from June 21, Mecca aside.
In Mecca the curfew will be lifted between 6:00am and 3:00pm until June 20, and thereafter the curfew will be shortened by a further five hours.
Saudi Arabia has reported more than 85,000 coronavirus infections and 503 deaths from COVID-19.
In March, it suspended the year-round "umrah" pilgrimage over fears of the disease spreading in the holy cities of Mecca and Medina.
That suspension will remain in place until further notice, the interior ministry said.
Authorities are yet to announce whether they will proceed with this year's Hajj -- scheduled for late July -- but they have urged Muslims to temporarily defer preparations for the annual pilgrimage.
Last year, some 2.5 million faithful travelled to Saudi Arabia from around the world to participate in the Hajj, which Muslims are obliged to perform at least once during their lifetime.