Thousands flooded The Mall, waving flags in the brilliant sunshine to celebrate the Queen's 70-year reign.
The 96-year-old watched a flypast with 17 other royals and was immediately flanked by Prince Charles and four-year old great-grandson Prince Louis.
The Queen looked delighted as she and Prince Louis chatted during the event.
But the noise of the 70-aircraft flypast was too much for the young prince, who was pictured covering his ears and tightly shutting his eyes.
The parade marked the start of a long bank holiday weekend of events celebrating the Queen's reign - the longest by a British monarch.
Riding on horseback and wearing the Platinum Jubilee medal with his uniform, the Prince of Wales inspected the troops in his mother's place.
The Queen, who was using a walking stick, has limited her appearances in recent months due to mobility issues.
As the soldiers marched towards Buckingham Palace at the end of the parade, the Queen emerged on to the balcony, accompanied by cheers from the crowd.
More than 1,500 officers and soldiers along with 350 horses from the Household Division took part in Trooping the Colour, the first time the parade has been staged in full since the pandemic.
After the parade, more than 70 aircraft - including Spitfires from World War Two, Apache helicopters, Typhoons and the Red Arrows - took part in the flypast over Buckingham Palace.
Several jets flew in formation to form the number 70 in honour of the Queen's long reign
Prince Charles, the Duchess of Cornwall, the Princess Royal, the Duke and Duchess of Cambridge and their three children - Prince George, Princess Charlotte and Prince Louis - flanked the monarch on the balcony - the Royal Family's first gathering there since 2019.
It had been decided only "working royals" would appear, which excluded the Duke and Duchess of Sussex, and the Queen's son, the Duke of York.
Prince Andrew, whose royal titles were returned to the Crown amid a lawsuit in the US, did not attend. He had been due to attend Friday's thanksgiving service, but on Thursday afternoon Buckingham Palace said he would miss it as he had tested positive for Covid.
Prince Harry and Meghan, who now live in the US, watched Trooping the Colour from a vantage point in the Duke of Wellington's former office, overlooking Horse Guards Parade.
They travelled with their children Archie, three, and Lilibet, who turns one on Saturday. Lilibet is the family nickname for the Queen.
Prince Harry and Meghan have been keeping a very low profile and seem to be carefully avoiding any accusations of stealing the limelight.
The Duke and Duchess of Sussex were pictured watching the Trooping the Colour ceremony from windows above Horse Guards Parade, but mostly stayed out of sight.
Since they weren't part of the Buckingham Palace balcony scene or in the carriage procession, they've largely remained under the radar and away from centre stage.
That's probably what Buckingham Palace most wanted. Because the couple attract so much public interest, both positive and negative, it could drown out the focus on the Jubilee events.
This might be about building bridges rather than making headlines, because they would have been made aware of the damage of any attention-grabbing comments or appearances.
But they are expected to be at St Paul's on Friday for the service of thanksgiving - and there is speculation about private meetings with the Queen over the weekend.
It's their daughter Lilibet's first birthday on Saturday, so it could all align for a family gathering.
Space for public viewing filled up by mid-morning. Thousands of spectators lined the Mall and filled nearby St James' Park, waving flags and draped in union jacks.
Many in the crowd saw the day as a historic moment, and spoke of their admiration for the Queen.
"She's such a strong personality," said Salamath Silmy, from north London. "I always talk to my daughter about how we have to be strong like her."
Visiting from the US, Elaine Henderson said the day represented "everything I love about Britain".
The parade was also briefly interrupted by protestors, claimed to be from animal rights and climate campaign group Animal Rebellion. Police arrested 12 people for obstruction of the highway.
Millions of people are gearing up for street parties among other celebrations over the four-day Bank Holiday weekend.
The Queen led the lighting of the principal Jubilee beacon in a special ceremony at Windsor Castle.
However, she will not attend Friday's Jubilee service at St Paul's Cathedral after experiencing discomfort at Thursday's ceremony, Buckingham Palace said, adding the decision had made with "great reluctance".
Prince Charles and Camilla also appeared in an episode of TV soap EastEnders, on BBC One. The royal couple joined the the fictional residents of Albert Square at their Jubilee street party, in scenes filmed earlier this year.
At the concert, heir to the throne Prince Charles and his son, the Duke of Cambridge, will pay tribute to the Queen who will be watching on television.
On Sunday there will be street parties, picnics and barbecues across the UK with more than 85,000 Big Jubilee Lunches planned.
The finale of the weekend will be the Jubilee Pageant which will make its way through the streets of the capital with a cast of 6,000 performers and close to 200 celebrities.
It will end with Ed Sheeran singing the national anthem with a choir made up of "national treasures" outside Buckingham Palace.
On Wednesday, the Queen thanked the public for organising celebratory events and said "many happy memories" would be made.
"I continue to be inspired by the goodwill shown to me, and hope that the coming days will provide an opportunity to reflect on all that has been achieved during the last 70 years, as we look to the future with confidence and enthusiasm," she said in a statement.
It was the first full Trooping the Colour since 2019
A royal gun salute was fired from Edinburgh Castle - with others in Cardiff Bay and Hillsborough Castle