Police escorted the remaining 50 demonstrators from the building's forecourt on Saturday afternoon, hauling some of them away after they refused to leave.
Up to a thousand other protesters remained camped outside the government complex, booing the police through the fence as they began rounding up the remaining demonstrators.
"Police should catch thieves, not students!" the crowds shouted. The early hours had seen the tensest scenes yet in a string of recent protests, with riot police using pepper spray to clear out more than 100 people who had pushed into the grounds of the complex, some of them scaling a high fence.
Police had dragged many away overnight and into the morning, making 13 arrests.
Student groups have been spearheading a civil disobedience campaign this week in response to Beijing's announcement last month that it will choose who can stand in elections for Hong Kong's leader in 2017.
More than 2,000 protesters, many of them secondary school pupils and university students, had protested at the city's main government headquarters on Friday, culminating with around 150 demonstrators breaking through police lines to occupy its forecourt late on Friday night.
Police said the 13 arrested were aged between 16 and 35 and detained for forcible entry into government premises, disorderly conduct in public place and assaulting a police officer.
Among those arrested was a prominent student leader, 17-year-old Joshua Wong.
Protesters had used umbrellas to protect themselves from being pepper-sprayed by police wearing riot gear including helmets and body-length plastic shields.
"This is an amazing turning point," Suki Wong, a recent graduate who works as an accountant, told AFP.
"Hong Kongers usually just lay there and do nothing. This time we're really making an impact."
Lu Yiu, 20, said his throat and nose burned from the pepper spray. "Everyone was crying as we were pushed onto the street from the extreme use of force," said Lu, who spent nine hours caught between police lines unable to use the toilet or sleep.
In a statement, the government "expressed regret" that protesters had stormed the complex, saying security personnel, police officers and protesters had suffered injuries but without giving details.
Friday's action was supposed to be the culmination of a week of protests that began on Monday when 13,000 students gathered on a campus in the north of the city, according to organisers.
On Thursday night, more than 2,000 people took their protest to the residence of Hong Kong's leader Leung Chun-ying with the hope of speaking to him, but he has so far refused to speak to the students or meet their leaders.
The protest comes after China last month said Hong Kongers would be allowed to vote for their leader for the first time in 2017, but that only candidates approved by a pro-Beijing committee could stand.
A protest in July saw half-a-million-people — according to organisers — take to the streets to express their discontent at what they see as China's increasingly tight grip on the city.
Handed back to China by former colonial ruler Britain in 1997, Hong Kong is governed under a "one country, two systems" agreement that grants civil liberties not seen on the mainland, including free speech and the right to protest.
But tensions have been rising in the southern Chinese city over fears that these freedoms are being eroded.
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