On Tuesday, Prime Minister Hwang Kyo-ahn told a government meeting the country had not seen a new MERS case in more than three weeks.
More than 16,000 people had been isolated at hospitals and homes as the government attempted to thwart the spread of the disease, and the last person was lifted from quarantine on Monday.
Twelve people remain hospitalised in South Korea and under treatment for MERS although only one was still testing positive for the virus, the health ministry told Reuters.
"It is the judgement of medical experts and the government that people can now feel safe," Hwang said in the meeting, according to the prime minister's office.
MERS was discovered in 2012 and the cases had been mostly centred in Saudi Arabia before the outbreak in South Korea.
The MERS virus belongs to the family of coronaviruses that includes the common cold, and can cause fever, breathing problems, pneumonia and kidney failure.
Experts say South Korea's overcrowded emergency rooms and hospital wards might have contributed to a wider-than-expected transmission of the virus, which usually spreads poorly between people.
South Korea's habits of "doctor shopping", or visiting multiple facilities to treat the same infection, and having many friends and family members visit hospitalised patients also might have contributed.
The public alarm over MERS rattled South Korea's economy, which posted its slowest quarterly growth in more than two years in the three months to June.
The Bank of Korea partially blamed the slowed growth on sapped consumption as foreign tourists cancelled visits and people stayed home in fear of infection.