A 58-year-old woman, who had been treated as a suspected case of MERS, died of acute respiratory failure on Monday and tests later came back positive for the virus.
The other victim was a 71-year-old man who had been confirmed to have the virus several days ago. The Yonhap report did not say when the man died.
Yonhap news agency today said that 25 people have now been diagnosed with the virus, the emergence of which has triggered widespread public alarm.
South Korea's first case was reported on May 20 and the health ministry said Monday that a total of 682 people who were exposed directly or indirectly to the virus have now been quarantined or put under special observation.
More than 20 countries have been affected by the virus, which has no known cure or vaccine, with most cases in Saudi Arabia where it has claimed more than 400 lives since 2012.
Health officials were particularly criticised for allowing an infected man to travel to China last week despite warnings from doctors.
The 44-year-old left on a business trip on Tuesday, a day after his father was diagnosed with the virus, and was confirmed Friday to have been infected himself.
The man flew to Hong Kong before travelling on to the Chinese city of Huizhou, where he is being treated under quarantine.
The current outbreak has been traced to a 68-year-old man diagnosed after returning from a trip to Saudi Arabia.
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