The protesters, who occupied the building since Monday, had said they would leave Friday night.
But early Friday, police entered the building and arrested 65 people, including about 24 who were not students, said UC Berkeley spokesman Dan Mogulof. The protesters face misdemeanor trespassing charges.
Another person was arrested outside and faces a charge of inciting.
Police decided to take action after protesters began breaking into locked classrooms and publicizing an all-night hip-hop party Friday.
"A peaceful protest is one thing, but it was becoming something altogether different," Mogulof said. "The red line for us is when these actions begin to interfere with the rights of other students."
No major damage was reported at Wheeler Hall. Classes were scheduled to be held there Friday.
Student protesters said they were caught off-guard by the raid and complained the police had not warned them.
"Police burst in while people were sleeping and immediately started locking doors and arresting people," Elias Martinez, an undergraduate political science major, said in a statement. "There had been cops in here all week, they were acting like it was OK. We had no idea."
On Thursday at San Francisco State University, police arrested a dozen people who had barricaded themselves inside a classroom building to protest budget cuts and fee hikes.
The two incidents are the latest in a series of demonstrations in which students have taken over buildings at California State University and University of California campuses to protest campus cuts and rising fees