The bailiffs, backed by police, dismantled barricades outside Citic Tower after the building's owners complained about the disruption and were granted a high court injunction.
The student protesters did not resist the clearance, and many helped to remove tents and fences.
The high court has also authorised the clearance of the Mong Kok site.
A third protest camp remains at Causeway Bay.
The activists have been on the streets since early October to protest against a decision by China to screen candidates for Hong Kong's 2017 leadership election. Numbers were originally in the tens of thousands but have fallen to a few hundred.