A driver was killed after a 10-metre-high (33 ft) roadside wall collapsed on top of a moving vehicle on Wednesday in Osan, some 44 kilometres (27 miles) south of Seoul, fire agency officials said.
Another person was found with no heartbeat in a flooded car in Seosan, South Chungcheong province, and could not be revived.
As of 5pm (0800 GMT), some parts of the South Chungcheong region further south of the capital had seen more than 400 millimetres (15.7 inches) of rain since Wednesday, the Ministry of the Interior and Safety said.
The downpours resulted in record rainfall in the area, and more wet weather was forecast for Thursday night, the Korea Meteorological Administration said.
Landslide alerts were raised to the highest level for several regions, including Chungcheong, as the heavy rains continued, according to the Korea Forest Service.
In the city of Gwangju, some 267 kilometres (166 miles) south of Seoul, 87 roads and 38 buildings were submerged within about two hours after torrential rain warnings were issued, according to the Yonhap News Agency.
Some 403 schools were closed and 166 reported property damage from the heavy rain on Thursday, the Ministry of Education said.
Reuters