Occupy London was last week refused permission to appeal against a High Court decision to allow their eviction to proceed.
The City of London Corporation said it "regretted" that it had become necessary to evict the protesters.
Occupy London, which campaigns against corporate greed, set up the camp on 15 October.
BBC correspondent Jeremy Cooke at the scene said there was a makeshift wooden platform set up by the protesters.
These were being used in a stand-off with police by a small number of protesters.
The High Court decided that the City of London Corporation's move to evict the camp was "lawful and justified".
The Court of Appeal's decision not to allow an appeal meant the corporation was free to clear the site.
The protesters insist they have a right to be at the site because the High Court orders refer only to the removal of tents and equipment.
George Barda, one of the five protesters who appealed against the High Court's decision, told the BBC he had "mixed emotions".
But he said: "It's not the beginning of the end, it's the end of the beginning.
"My personal concern is that we don't allow the drama of this event to eclipse the huge and important issues that we in this country and billions across the world are increasingly facing.
"And I have no doubt that as the economic situation gets worse in the coming years, more and more people will be joining this movement."
There was also an eviction of an Occupy campaign site, which campaigners say is a legally occupied squat, at Featherstone Street in Islington, north London.
"We regret that it has come to this but the High Court Judgment speaks for itself and the Court of Appeal has confirmed that judgment.
"High Court enforcement officers employed by the City of London Corporation are undertaking the removal with the police present to ensure public safety and maintain order. We would ask protesters to move on peaceably.
"The City of London Corporation is ensuring vulnerable people are being helped and supported to find appropriate accommodation in partnership with Broadway, a charity for the homeless."
A statement from City of London Police said: "At 12.10 tonight, bailiffs employed by the City of London Corporation began enforcing a High Court order for the removal of tents and equipment outside St Paul's Cathedral.
"Officers from the City of London Police supported by Metropolitan Police are present to ensure public safety, maintain order and facilitate lawful protest."