The two men -- aged 84 and 87 -- died from Sunday night to Monday morning of Middle East Respiratory Syndrome, the health ministry said, adding both had been battling cancer.
They contracted the virus at Samsung Medical Centre in Seoul and Daecheong hospital in the western city of Daejeon and were diagnosed on June 9 and 12, respectively.
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The three included two patients at Samsung hospital and Konkuk University Medical Centre in Seoul and one caregiver at Daecheong hospital.
Samsung -- a major hospital where more than 80 patients, families and medical workers have been infected -- suspended most services on June 14 to stem the spread of the virus.
Fourteen patients were in critical condition, the ministry said, adding 50 people had recovered and were released from hospital so far, including seven from Saturday to Sunday.
The spread of the virus has slowed since the first two weeks of June, when the number of patients often grew by double digits including a daily record of 23 on June 7.
On Saturday the authorities reported no new cases for the first time in 16 days.
The outbreak began on May 20 when a 68-year-old man was diagnosed after returning from a trip to Saudi Arabia.
Since then the potentially deadly virus had spread at an unusually rapid pace, sparking public alarm that prompted the temporary closure of thousands of schools and trip cancellations by more than 120,000 foreign tourist.
Most schools have reopened except for five in Gyeonggi province surrounding Seoul, the southern port of Busan and the southeastern city of Daegu.
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