A former squat in the city's southern Friedrichshain area, which was evicted this time last year, was attacked by a group of 100 people at around 00:30 on Sunday morning.
When the police arrived at the Liebigstrasse 14 building, the group ran off into the side streets of the area which is known for left-wing communes.
Some set fire to a van and smashed the windows of two banks with bricks, the Berliner Zeitung newspaper reported on Sunday.
“The willingness to use violence within the extreme-left scene remains high,” Berlin state interior minister Frank Henkel told the paper. “The police won't let themselves rise to this obvious provocation.”
In the nearby Rigaer street, police stormed a left-wing squat above a bar popular with residents of the building and other left-wingers from the area.
When police tried to enter the commune, guests at the bar threw bottles at them, prompting officers to use pepper spray.
Those in the bar, known as Kadterschmiede, were holding a meeting about an upcoming demonstration against a European police conference being held in Berlin in February.
Also on Saturday, 1,000 protesters gathered in the Neukölln district to protest police violence – and some rioted and smashed several shop windows after officers broke up the demonstration.
The Berlin squatting and left-wing scene erupted in anger last February after the squat “Leibig 14” – named after its street address – was evicted by police.
The building is being renovated and will be turned into apartments, further fuelling local anger at gentrification.