The South's disaster management office said 122 houses were flooded or partly destroyed, leaving 263 people homeless.
A 57-year-old man was found dead after being swept away in a flooded stream in the northern border city of Pocheon, it said.
In Hongcheon, east of Seoul, a 85-year-old man was killed in a landslide, while a 34-year-old man went missing on a flooded road in Gapyeong, the office said.
Torrential rains knocked down two sections of the barbed wire fence along the border with North Korea, one of them 192 metres long, the South's defence ministry said.
The North's Korean Central News Agency reported Saturday that two people were killed and hundreds left homeless. Updated figures have not been given.
Poor weather makes it harder for the communist state to feed its 24-million-strong population as it lacks advanced agricultural technology and infrastructure.