The protest against Israel's attacks on Gaza saw one police officer knocked unconscious and two others receive facial injuries, a police spokesman said.
An initially peaceful demonstration ended with a group of protesters facing mounted riot police throwing missiles and smashing windows on Kensington High Street near the Israeli Embassy.
Riot officers from the Metropolitan Police force charged at the group of mainly young men.
Sticks and barriers were hurled at the officers by the group, many of whom were masked.
About 300 police in full riot gear had surrounded a similar-sized group of protesters pushing them up the street.
Three people were arrested, police said.
Police ensured a heavy presence at today's demonstration after a similar protest in the capital last Saturday was also marred by confrontations.
The Metropolitan Police estimated 12,000 people joined in Britain's biggest pro-Palestine demonstration in London's Hyde Park today before marching through the capital to the embassy, chanting "free, free Palestine".
Shoes were thrown during the march in the capital, and were also hurled by demonstrators in Edinburgh protesting against the rising death toll and suffering of civilians in Gaza.
Actress Lauren Booth criticised her brother-in-law Tony Blair, saying his suggestions for a ceasefire in Gaza would condemn Palestinians "to a slow agonising death".
Cherie Blair's half-sister Ms Booth said: "Tony Blair's only comment regarding the ceasefire has been to say that it can only take place after the tunnels in Gaza are destroyed.
"What he is suggesting means that after the massacre people will have no access to food, kerosene and medicines that came through those tunnels. That is not a ceasefire, that is a slow agonising death."
Eurythmics star Annie Lennox said she was taking an "humanitarian stance".
"I do not believe in a militaristic approach," she said. "It's very important that people in society at large see that we can use our voices collectively."
Organisers of the march brought together a number of different groups including Stop The War Coalition, The British Muslim Initiative and the Palestine Solidarity Campaign.
John Rees, co-founder of the Stop the War Coalition, said: "Unless we are able to deal with this we will not get peace in the Middle East."
Many of the protesters trapped between two lines of riot police were peaceful and included women and older people. But their pleas to those causing disorder to "stop throwing things" and sit down were ignored.
There were running skirmishes between the lines of police and groups of young men, each time prompting a further charge from the officers and sending the crowd running screaming in the opposite direction.
A Met spokesman said that from 3.20pm, officers came under "sustained attack from a group of protesters who started trying to push over the barriers placed there to protect the embassy".
He said: "The barrier line put in place to protect the embassy was dismantled and a hard core of protesters threw missiles, including sticks stones and metal barriers, at police."
Extra officers were deployed at 4.40pm, but this group was then attacked by the "hard core" of protesters, he added.
Police estimate the crowd was between 15,000 and 20,000 at its peak, although it was starting to disperse tonight.
Commander Bob Broadhurst said: "A group of people on this demonstration have set out to deliberately confront and antagonise police officers trying to protect the Embassy of Israel.
"We are very disappointed by the irresponsible and criminal actions of those who have challenged police by ripping apart security barriers and throwing objects at them. A hard core of demonstrators are undermining the cause of the vast majority of people on this demonstration, who are law abiding citizens wishing to protest peacefully."
Of the three arrests, one man was held on suspicion of assaulting a police officer and another man was in custody on suspicion of aggravated trespass.
The spokesman said they were awaiting details of the third arrest.
In Edinburgh, three officers were injured after being attacked by a group of 60 protesters outside the US Consulate.
A Starbucks coffee shop in the area where the protesters were penned was stripped of chairs and had its front windows smashed.
Protesters also removed fittings from the shop.
Residents living in flats above watched the scenes from their windows.
Many people were pleading with police to let them out of the cordon.
Nick Napier, organiser of the Edinburgh protest, said the action was taken as a result of the "rage and anger" over the death toll in Gaza over the past two weeks.
"People are here because they know the trail of blood leads from Gaza back to Britain and that Gordon Brown, while publicly calling for a ceasefire, we know has instructed his diplomats in New York to support the Americans," he told Sky News.
"They're angry. It's another year, another war, another massacre."
A spokesman for the US Consulate declined to comment.
People in Newcastle also demonstrated today, while tomorrow more than 3,000 are expected to attend a pro-Israel rally in Manchester.
The demonstration will call for an end to "Hamas terror and peace for the people of Israel and Gaza".
Organised by the Israel Information Centre (IIC) in Manchester, speakers include the former Rochdale MP Lorna Fitzsimons, now chief executive of the Britain Israel Communications and Research Centre.
Representatives of the Christian Friends of Israel and the Council of Christians and Jews are also expected to attend the rally in Albert Square, Manchester, at 11am.
Heavy fighting continued in Gaza today and Israeli forces dropped leaflets warning of an escalation in attacks on Gaza City.
There were reports that the violence did not stop during a three-hour ceasefire intended to allow in humanitarian aid.
Charities condemned the violence and said the temporary respites were not long enough to get desperately-needed food and medical help to residents, many of whom are without electricity and running water.
More than 800 Palestinians have been killed since the attacks began two weeks ago.
Protesters accused the police of failing to manage the crowd properly as attempts were made to clear the area.
One woman, who would give her name only as Sadia, said she had to be helped out of the crowd and her friend fainted after the situation got "completely out of hand"
The 33-year-old from Fulham, west London, who works for a human rights organisation, said: "I got lifted from the ground and I thought that was it.
"It was really dangerous - they started pushing and we were trapped.
"The police were standing there and not doing anything."
Another witness caught up in the trouble said police did not appear to realise the severity of the situation as people were pushed against barriers.
"The police tactics led to people being crushed," said the 33-year-old Londoner.
A Met Police spokesman denied the situation had been poorly handled.
"When you've got 12,000 demonstrators and a few hundred officers it can be difficult," he said. "We apologise if innocent people got caught up in it."
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