Bailiffs had already moved in to remove barricades around the protest camp in the heart of the business district, but despite the police order a hard core of a few hundred refused to leave.
Crowds shouted demands for free leadership elections a cause which has underpinned the demonstrations and vowed the clearance operation would not end a campaign they say has redefined the city's vexed relationship with Beijing.
Police announced a "lockdown" of the area after a 30-minute window in which protesters could voluntarily leave the site an encampment of tents, supply stations and art installations sprawling along a kilometre of multi-lane highway.
"Police will lock down the occupied area and set up a police cordon area... If anyone refuses to leave police will take action to disperse or arrest," said senior officer Kwok Pak-chung.
Thousands gathered on Wednesday night for one final mass rally at the Admiralty site, but the numbers had dwindled by morning, leaving just a few hundred sitting in the road, including pro-democracy lawmakers.
"This is not the end of the movement. The political awakening amongst the young is irreversible and we will fight on,"pro-democracy lawmaker Claudia Mo told AFP earlier Thursday.
The bailiffs who descended with cutters and pliers to take down barricades and load them into trucks were serving court orders taken out by transport companies frustrated at the long-running disruption.
Many protesters had packed up their tents and left by Thursday morning, but left hundreds who said they intended to stand their ground.
"I'm not tired (of the campaign). I'll never be tired, only the government is tired," said 19-year-old student Alice.