Onnuri Church, one of the biggest churches in Seoul, required members to sign up online ahead of the service and sit on designated seats to maintain distance.
It has also limited attendance to 700 in a hall with a capacity of 3,000 people, a church official said.
Last Sunday, South Korea extended its social distancing policy until May 5 but offered some relief for religious and sports facilities previously subject to strict restrictions.
A secretive church, the Shincheonji Church of Jesus, was at the epicenter of South Korea's coroavirus outbreak, with about half of the country's total infections of 10,728 linked to its members.
South Korea managed to curb the first major outbreak outside China with massive testing and aggressive contact tracing but there have been a series of small outbreaks involving churches and other clusters.
South Korea on Sunday reported 10 new cases, marking the eight day when the number of new infections hovered around that level.
Church members expressed faith in the ability by South Korea and churches to tackle the coronavirus outbreak.
“I did not have fear. I believed that the church would abide by safe principles and resume worships,” Kang Hye-mi, a 29-year-old worshiper, said at Myeongdong Catholic Cathedral in Seoul.
When restrictions were put in place, South Korean churches turned to online or drive-in services where churchgoers attended by parking their cars on school playgrounds.
Yang Sun-kyung, who went to the Onnuri church for the first time in two months, said she is able to concentrate better when attending church rather than during online worship which was sometimes distracting.
She said churches are a “very safe” place, but people should refrain from going to bars and clubs, which are “very dangerous."
"I hope this (our church) can be an exemplary case for others. And I hope the coronavirus would end as soon as possible,” Han Jin-gun, a 34-year-old worshiper at Onnuri said.