Among the victims were an elderly woman and a young girl.
The strength of the floods overturned cars, closed roads, damaged homes and forced hundreds to leave their properties.
The hardest hit areas were the provinces of Malaga and Almeria, and Murcia region.
At least 600 people had to be evacuated from their homes in Andalucia region, which contains Malaga and Almeria, officials said.
Spain’s weather agency said that up to 245 litres (65 gallons) of water per square metre had fallen on Friday morning alone.
An elderly woman died when a river broke its banks and floodwater hit her home in Alora, north of Malaga, AFP reports.
Two other adults died in Andalucia, while three others, including a 10-year old girl were killed in neighboring Murcia.
“In Malaga province there are 800 staff working to return things to normal as quickly as possible. The rains are decreasing and seem to be shifting towards Granada and Almeria,” a regional government spokesperson told AFP.
However, torrential rain and violent thunderstorms are predicted to continue in the south of the country during the weekend.
The heavy rains in parts of the south follow months of drought and high temperatures across Spain which triggered dozens of wildfires.
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