A committed core of around a dozen demonstrators had staged a sit-in at the centre of the last site in the busy shopping district of Causeway Bay as police cut away barricades and tore down banners and shelters.
Seventeen people, from students to the elderly, were arrested without resisting, with some shouting "We will be back" and "Fight to the end".
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Activists calling for free leadership elections occupied major traffic arteries after China said in August that candidates for the city's chief executive elections in 2017 would first be vetted by a loyalist committee.
Campaigners said the move would ensure a pro-Beijing stooge in the leadership role.
Police demolished the city's main protest camp last week.
"Following the completion of clearance work in Causeway Bay Occupy area, the episode of illegal occupation activities for more than two months is over," chief executive Leung Chun-ying told reporters today.
He said that the demonstrations had led to "serious losses" in sectors including tourism and retail.
"Other than economic losses, I believe the greatest loss Hong Kong society has suffered is the damage to the rule of law by a small group of people," he added.
Leung is vilified by protesters who cast him variously as a wolf and a vampire and have repeatedly asked for him to step down.
But Beijing has backed his administration throughout the occupation.
"If we just talk about democracy without talking about the rule of law, it's not real democracy but a state of no government," Leung said.
Causeway Bay hosted the smallest of the three camps that sprang up in late September, paralysing sections of the city, as part of the student-led campaign for free leadership elections.
The main Admiralty camp which sprawled across a kilometre of multi-lane highway through the heart of the business district was cleared on Thursday.
Police cleared the other major protest site in the working-class commercial district of Mongkok - scene of some of the most violent clashes since the campaign began - in late November.
Students who spearheaded the street protests were among the sit-in group in Causeway Bay today.
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