The Catholic Church has an estimated 5,8m members in the country.
Major Protestant groups have also halted Sunday services. All Buddhist events have been called off.
South Korea is battling the worst coronavirus outbreak outside China, with 3,736 cases and 18 deaths so far.
Religion is at the centre of South Korea’s outbreak. Authorities say members of the fringe Christian group Shincheonji Church infected one another in the southern city of Daegu last month, before fanning out around the country.
More than 85,403 cases of the new coronavirus have been confirmed in over 50 countries, according to the World Health Organization.
The global death toll is more than 2,900. The vast majority of infections and deaths are in China.
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On Sunday, Australia and Thailand also recorded their first fatalities from coronavirus.
A 78-year-old Australian man died after being infected on the Diamond Princess cruise ship in Japan last month.
Thailand, which has had 42 cases of the virus, said a 35-year-old man who died was also suffering from dengue fever.
The Catholic Church – one of the main religious communities in the country – has suspended Masses in all its 1,734 parishes until 7 March.
The Church had never taken such a step in 236 years of presence in South Korea.
The country’s Buddhist organisations cancelled events earlier this week. Major protestant churches are holding Sunday services online.
In the capital Seoul, worshippers were turned away from the Yoido Full Gospel Church, which posted a sermon for its 560,000 followers on YouTube, Reuters news agency reported.