Counter demonstrations were also taking place, with dozens of people with Union flags standing close to the Cenotaph on Whitehall, drawing chants of “shame on you” from pro-Palestinian marchers.
Two people have been arrested so far by officers policing the protest.
One man was arrested on Whitehall after a police officer was assaulted, the Metropolitan Police announced on X, formerly Twitter.
The force said the officer was taken to hospital following the incident.
Another man was arrested in Waterloo Road on suspicion of a racially aggravated public order offence and making threats to kill.
A Section 60 and Section 60AA authority was put in place until midnight, giving police stop and search powers in the London boroughs of the City of Westminster and Kensington and Chelsea.
A Section 60 AA requires a person to remove items that might be used to conceal their identity, such as masks.
Police were seen clashing with pro-Palestinian protesters.
Officers appeared to be detaining someone close to Downing Street before demonstrators began scuffling with them.
Punches and kicks were thrown and officers ordered the demonstrators to move away.
One person was taken to the floor and carried away to chants of “let him go” from other protesters.
Cries of “Allahu akbar”, the Arabic phrase for “God is great”, also rang out.
Demonstrators gathered at noon on Saturday in London with banners and posters and let off fireworks and red and green flares.
Some chanted “from the river to the sea, Palestine will be free”, despite controversy around the slogan’s meaning.
A woman was knocked over by a police horse after the animal was startled by fireworks, but appeared to be fine when she was brought back to her feet.
More than 200 people staged a sit-in on the concourse of London Waterloo station, chanting “ceasefire now”, according to activist group Sisters Uncut.
More than 1,000 Met Police officers are on duty for the demonstration, the force announced on X.
The Met said it expected large crowds around Embankment, Westminster and Waterloo Bridges, the Strand, Whitehall and nearby roads.
It warned the force would be vigilant in responding to crime.
“There is absolutely no place in London for hate crime,” the Met said on X.
“Officers will respond to any criminality where they see it and take decisive action, but there may be things not seen in the moment.
“We’ll also be reviewing CCTV and images/video shared by the public to identify offences.”
Several conditions have been imposed under the Public Order Act, including that protesters should follow a specified route and should not gather in a specified area outside the Israeli Embassy.
A protest is due to take place in Bristol city centre on Sunday.
Avon and Somerset Constabulary said it was expecting between 2,000 and 5,000 people to gather.