Two days of torrential rain flooded streets and subway stations in the capital, with President Yoon Suk-yeol saying it was the heaviest rainfall since Seoul weather records began 115 years ago.
Images shared on social media earlier this week showed people wading through waist-deep water and overflowing metro stations, with the posh Gangnam district particularly hard hit.
Of the 11 dead, six were in Seoul, three in Gyeonggi province and two in Gangwon province, according to data from the interior ministry. Three of the eight missing were from the capital.
More than 5,300 people were forced to evacuate their homes, the ministry added.
Among the 11 victims, three died while trapped in their flooded semi-basement apartment, known as a banjiha, according to the ministry. Local reports say the victims were a teenager, her mother and her aunt.
One victim is believed to have been electrocuted while removing a tree that had fallen onto a sidewalk while another died when a landslide buried his home in mountainous Gangwon.
At an official meeting on relief efforts, South Korean Prime Minister Han Duck-soo said the government had already completed the bulk of emergency repair work.