Police in Malmo said they were pelted with rocks and dozens of cars were set on fire, including in an underground garage, and described the events that started on Sunday and lasted overnight as "a violent riot".
The clashes started after an anti-Islam activist, Salwan Momika, burned a copy of the Koran on Sunday and an angry mob tried to stop him, police said.
At least three people were detained, they said.
Early on Monday, a crowd of mainly young people set fire to tyres and debris and some threw electric scooters, bicycles and barriers in Malmo's Rosengard neighbourhood, which has been the scene of similar clashes in the past.
Several banners condemned the Koran burning.
"I understand that a public gathering like this arouses strong emotions but we cannot tolerate disturbances and violent expressions like those we saw on Sunday afternoon," senior police officer Petra Stenkula said.
"It is extremely regrettable to once again see violence and vandalism at Rosengard," she said.
"Regardless of the reason behind these riots, the car fires, the harassment, violence against police officers... regardless of the reason, I think that all Swedes find this completely unacceptable," Swedish Prime Minister Ulf Kristersson said at a news conference.
In the past months, Momika, a refugee from Iraq, has desecrated copies of the Koran in a series of anti-Islam protests mostly in Stockholm.
Swedish police have allowed his actions, citing freedom of speech.
The Koran burnings have sparked angry protests in Muslim countries, attacks on Swedish diplomatic missions and threats from Islamic extremists.
Muslim leaders in Sweden have called on the government to find ways to stop the Koran desecrations.
Sweden dropped its last blasphemy laws in the 1970s and the government has said it has no intention to reintroduce them.
However, the government has announced an investigation into the possibility of enabling police to reject permits for demonstrations over national security concerns.
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