Typhoon Ewiniar was headed out to sea after it came over the Korean peninsula on Monday, first striking the southwest coast, and then heading on a northeast track.
It dumped as much as 26 cm (10.2 inches) of rain in South Kyongsang province, in the southern part of the country, weather officials said.
Four people died on Sunday as the storm was approaching the country. A woman died on Monday after she was swept away in a swollen river and another woman died while saving her son from flood waters, the National Emergency Management Agency said.
Three people were missing. Flood waters covered some 15,000 hectares (37,000 acres) of farm land and damaged about 625 homes, agency official Lim Tae-wan said.
Domestic transport was disrupted as airlines cancelled several flights and traffic on highways came to a near standstill as the storm passed.
Typhoon Ewiniar triggered heavy rains in China, prompting the evacuation of cities along its eastern coast on Saturday.