The country reported 4,944 new Covid cases, including 4,923 local infections, raising the total caseload to 4,62,555, according to the Korea Disease Control and Prevention Agency (KDCA), reported Yonhap news agency.
The number of critically ill patients came to 736, up from the previous record high of 733 on Thursday.
Friday's tally is down from 5,266 counted the previous day, which marked an all-time high since the country reported the first Covid case in January last year. The daily cases had stayed above 5,000 for two consecutive days.
The death toll came to 3,739, up by 34 from a day earlier. The fatality rate stood at 0.81 per cent.
The emergence of the potentially more transmissible variant is a setback to South Korea's efforts to return to normalcy with a gradual easing of virus restrictions under the "living with Covid" scheme that began last month.
Six omicron variant infections have been confirmed this week, and fears are growing that the cases will rise quickly.
Health authorities note that the number of critically ill patients, mostly the elderly, is growing fast, sparking concerns that the country's medical system could reach its limit.
As of 5 p.m. Thursday, 79.2 per cent of intensive care units were occupied across the country. The percentage for Seoul was 89.9 per cent.
More than 900 patients were on the waiting list for an ICU bed and 12,396 patients were undergoing at-home treatment.
To contain the spread of the omicron variant, the government said it will limit private gatherings to six in the capital area and eight in other regions for four weeks starting next week. Currently, the cap is 10 people in the capital area and 12 in other regions.
Authorities also extended the list of facilities requiring proof of vaccination or a negative test for entry. Restaurants, cafes, cram schools, movie theaters, public study rooms and museums are among the newly included places.
A one-week grace period will be allowed before enforcing the rules.
Teenagers aged between 12 and 17 will need to present the vaccine pass for entry into these facilities, starting in February next year, given that the vaccination rate among the age group is still low.
The country had planned to further relax the virus curbs later this month, but the government decided to put the scheme on hold, citing the high risks of the pandemic and variant concerns.
Beginning Friday, all international arrivals are required to undergo a mandatory quarantine for 10 days for the next two weeks, regardless of whether they are vaccinated.
Of the locally transmitted cases Friday, Seoul reported 2,094 new cases, and the surrounding Gyeonggi Province posted 1,464.
The number of cases from overseas came to 21, raising the total to 15,817.
The KDCA said 42.61 million people, or 83 per cent of the country's population, have received their first shots of Covid vaccines, and 41.19 million people, or 80.2 per cent, have been fully vaccinated.
About 3.57 million people, or 7 per cent of the population, have received a booster shot.