Scotland Yard said a 14-year-old girl and 17-year-old boy were detained at around 1.15pm in Westminster's Parliament Square on Friday.
The pair were arrested on suspicion of obstruction of a highway and taken into custody.
The arrests were made at the conclusion of the five day long Extinction Rebellion "summer uprising" that aimed to cause disruption in five UK cities.
Protesters targeted Bristol, Cardiff, Glasgow, Leeds and London, calling on the Government to take action on climate change.
On Monday, environmental campaigners brought a 25ft purple boat to Glasgow city centre, blocking the Trongate.
Around 100 people took part in the demonstration which ended in no arrests being made.
In Cardiff, campaigners parked a large green boat outside the castle cutting off traffic.
Tents were also set up on grass in front of Cardiff City Hall, the home of the Welsh capital's local government
A total of seven people were arrested and charged with aggravated trespass following demonstrations at construction sites in east London on Tuesday.
In Bristol, 16 people were charged in connection with a city centre protest on Wednesday which affected the M32.
The group, who have all been charged with wilfully obstructing a public highway, were bailed and were due to appear at Bristol Magistrates' Court on Friday.
Chief inspector Mark Runacres, from Avon and Somerset Police, said the protests had been "very challenging" for Bristol.
"A Memorandum of Understanding (MOU) was drawn up with protesters outlining what activity was acceptable and what we would not tolerate," he said.
"When this MOU was breached on Wednesday, a line was crossed and we took robust action."
Mr Runacres added: "We know the protesters' actions have been frustrating to many people, but along with our partner agencies, we've all done our best to pre-warn the public of potential disruption, keep people informed of protest activity, keep people safe and keep the city moving.
"The protest has had a significant impact on our resources. We've called in mutual aid, cancelled officers' rest days and extended overtime to deal with the demand we've been facing."
In London on Friday, the Metropolitan Police imposed a condition on protesters under the Public Order Act to prevent them using a boat, vehicle or "other structures" to disrupt the capital.
Brightly painted boats have become a feature of Extinction Rebellion protests, with a blue vessel bearing the message "Act Now" parked outside the Royal Courts of Justice on Monday.
More than 200 protesters gathered outside the courts in the Strand blocking the road to traffic in both directions.
Extinction Rebellion has called on the Met and the Crown Prosecution Service to drop the prosecutions of more than 1,000 protesters who were arrested during demonstrations at five London sites in April.
Around 180 of them have been charged so far.
But with another mass demonstration planned for October 7, the Met has pledged to do everything in its power to stop a repeat of April's large-scale disruption, which cost the force around £16 million.
Deputy assistant commissioner Laurence Taylor said: "I'm not going to sit here and say there are going to be no roads blocked, I can't promise that.
"We will do everything we can to try to avoid that. That includes engaging with protest groups, it will include putting conditions on where appropriate, it will include making sure we've got the appropriate planning and resources in place to deal with obstructions should they take place."