Officers later used "containment" then "controlled dispersal" and made temporary toilets and water available to protesters, police said.
At about 1800 BST, a small group of protesters faced a line of riot police in Threadneedle Street, near the Bank of England and the branch of RBS attacked earlier.
The BBC's Rob Broomby said demonstrators were "angry, but getting weary - they've been held in just a few narrow streets for a number of hours now".
A few protesters threw plastic bottles, banners and toilet rolls at police, amid chants of "Let us out, let us out."
Protesters had smashed RBS windows with missiles, including coins and computer keyboards, and entered the building. The branch had been closed already as a precautionary measure.
Mounted police and riot officers used shields to push demonstrators back and officers said they entered the RBS building just after 1400 BST "in support of building security".
Two people were arrested for aggravated burglary at the RBS, police say.
RBS has been in the spotlight after the £703,000 pension arrangement of former chief executive, Sir Fred Goodwin, sparked public anger.
By late afternoon, the BBC's Dominic Hurst said a branch of HSBC had also been attacked and had windows broken.
Police say CCTV footage and other video evidence will be reviewed to try to identify those involved in crimes.
Earlier, officers were pelted with empty beer cans, fruit and flour outside the Bank of England as the crowd of demonstrators had attempted to reach a peaceful climate change protest in nearby Bishopsgate.
Police said officers suffered only minor injuries during the protests, although one was admitted to hospital. Scotland Yard also said its response had been "proportionate".
Some of the protesters had been "provocative" and "determined to cause violence", claimed Met Commander Simon O'Brien.
Seven demonstrators were taken to hospital for treatment for injuries.
Riot police and protesters were caught up in an evening stand-off
Hundreds of Climate Camp demonstrators - behind direct action protests at Heathrow Airport and power stations in North Yorkshire and Kent - pitched tents in protest against carbon markets.
One organiser described it as a 24-hour camp and said they intended to stay until Thursday lunchtime.
But later in the evening some protesters wanted to leave but could not because they were penned in during a stand-off with police, the BBC's Ben Brown reported.
Earlier several hundred anti-war demonstrators marched to a rally in Trafalgar Square from the US Embassy in central London.
The BBC's Dominic Casciani said it had been "completely different" to the protests in the City, and demonstrators were in peaceful mood.
Crowds also gathered outside Buckingham Palace for the arrival of US President Barack Obama and his wife Michelle, who began a visit with the Queen shortly after 1700 BST.
The day began with protest groups under the G20 Meltdown banner marching to the Bank of England in the City urging those who had lost their homes, jobs, savings or pensions to join them in following four "horsemen of the apocalypse" to "lay siege" to financial institutions.
Many City workers have dressed in casual clothes after banks and other institutions were warned they may be targeted.
Protester Daniel Blinkhorn, from Brighton, was among those marching from London Bridge station to the Bank. He said the G20 leaders had a "real opportunity to green the global economy".
Housing association worker Tony Streeter told the BBC: "I'm here because I think people are angry about what's going on in the world there's too much greed."
At 2115 BST, Scotland Yard said there had been 63 arrests related to the protests on Wednesday, following four arrests on Tuesday.
The four people detained on Tuesday were charged after officers were alerted to a group trying to break into a building in the Holborn area of central London, police said.
On Wednesday, police questioned demonstrators travelling in an armoured vehicle dressed in helmets and overalls.
Police say 11 people have been arrested on suspicion of possessing police uniforms and for road traffic offences.
Six police forces are part of the £7.5m G20 security plan, led by London's Met.
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