While water levels decreased on Monday morning, many roads remain shut and buses and trains between Malmö and Ystad were severely disrupted. More than a thousand homes remain without electricity.
The heavy downpour has also affected lorries making deliveries to and from Denmark over the Öresund Bridge.
Emergency Services said they received over 400 calls on Sunday after over 100 millimetres of rain fell in just 36 hours. This is double the amount that normally falls across the month of August, according to meteorologist Therese Fougman, speaking to news agency TT.
In Malmö, hundreds of cars were completely destroyed when a garage flooded in the luxury Crown Prince skyscraper.
Several people had to be rescued after their cars filled up with water, others were spotted swimming away from their vehicles.
One woman in the city said she was close to drowning in an elevator that stopped and started taking in water.
"I pounded as hard as I could, screamed and shouted jumping," she told newspaper Sydsvenskan.
When the water reached up to her chest she kicked sharply on the elevator door and managed to force it open so that she could squeeze out.
Police have criticized drivers who broke traffic rules to avoid the flood waters.
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"People were stressed but it is an offence to drive on a bike path or go the wrong way on a highway," Communications Officer Stephan Soderholm told TT.
No further rain is expected in the coming days.
Photos: TT news agency