Port Elizabeth and Grahamstown were the hardest hit, with a road linking the two towns closed to traffic after a large part of it collapsed.
“Most of the flood victims drowned, other people died in a road accidents,” said John Fobian, a spokesman for regional disaster management.
Torrential rain began hitting the region on Friday, resulting in over a thousand people being evacuated from their homes and businesses. The town of East London was also affected.
“The damage caused to people homes, including the road that caved in is extensive. The rebuilding of the road is likely to take months,” said Fobian.
Between 2009 and 2010, large parts of the region recorded one of the worst droughts in almost 50 years, which saw the city Port Elizabeth enforce water restrictions.
Further showers were expected to continue until late afternoon, according to the weather service.