In a message to the nation, she thanked all those who organised the events.
Festivities culminated in an appearance by the senior royals on the Buckingham Palace balcony in front of huge crowds to watch an RAF flypast.
But the Queen's consort, Prince Philip, was absent from her side as he remains in hospital with a bladder infection.
The Earl and Countess of Wessex visited the Duke of Edinburgh on Tuesday afternoon.
Afterwards, Prince Edward said: "He's feeling better." The countess added: "He's in good spirits; he's on good form."
'Happy atmosphere'
The Queen's message was broadcast on television and radio across the UK and Commonwealth.
Continue reading the main story
Analysis
Daniela Relph
Royal correspondent
After Monday's party, today was a more sedate tribute to the Queen.
The Service of Thanksgiving at St Paul's Cathedral was a celebration of 60 years of loyal service and commitment.
In his sermon, the Archbishop of Canterbury spoke of the Queen's "years of utterly demanding yet deeply joyful service". His words are a reflection of the mood throughout the Jubilee celebrations.
Thousands again descended on central London for the ceremonial part of the weekend's festivities - especially the Royal Family's appearance on the balcony of Buckingham Palace.
I have spoken to many people over the past few days about how they view the Queen. Some have been royalists, some far from it. But nearly all have held the Queen in high regard.
The days events have been marked though by the absence of the Duke of Edinburgh. For 60 years he has been at the Queen's side at almost every ceremonial occasion. Today she has been without him.
"The events that I have attended to mark my Diamond Jubilee have been a humbling experience," she said. "It has touched me deeply to see so many thousands of families, neighbours and friends celebrating together in such a happy atmosphere.
"But Prince Philip and I want to take this opportunity to offer our special thanks and appreciation to all those who have had a hand in organising these Jubilee celebrations.
"It has been a massive challenge, and I am sure that everyone who has enjoyed these festive occasions realises how much work has been involved."
She added: "I hope that memories of all this year's happy events will brighten our lives for many years to come.
"I will continue to treasure and draw inspiration from the countless kindnesses shown to me in this country and throughout the Commonwealth. Thank you all."
Earlier on Tuesday, the Queen attended a thanksgiving service at St Paul's Cathedral where Archbishop of Canterbury Dr Rowan Williams paid tribute to her "lifelong dedication".
"I don't think it's at all fanciful to say that, in all her public engagements, our Queen has shown a quality of joy in the happiness of others," he said.
'Tireless leader'
David Cameron, who gave a reading at the service, called her "a real inspiration".
The Queen attended a Jubilee thanksgiving service at St Paul's Cathedral
"We have seen the country come together with a sense of celebration and unity but also tremendous resilience, resilience from people who want to celebrate despite the weather and resilience, of course, from Her Majesty - nothing stops her doing the job she does," the prime minister said.
US President Barack Obama was among those who payed tribute to her "60 extraordinary years".
In a specially recorded message he called the Queen "a steadfast ally, loyal friend and tireless leader" and said she had been "the chief source of resilience" for the unique alliance between his country and the UK throughout her reign.
In other Jubilee events on Tuesday:
Crowds gathered from early morning to cheer the Queen on her journey from Buckingham Palace to St Paul's
The congregation at the cathedral included a large representation from the government, military personnel and members of the royal household, alongside diplomats and foreign leaders
After the service, the Queen attended a reception at nearby Mansion House - the official residence of the Lord Mayor of London
The Prince of Wales and Duchess of Cornwall, the Duke and Duchess of Cambridge and Prince Harry were at a similar event at the Guildhall
All of the senior royals then enjoyed a lunch at Westminster Hall before embarking on a carriage procession through packed streets back to the palace
The day ended in an appearance by the senior royals on the palace balcony to watch a flypast by World War II aircraft and the Red arrows
The flypast had been threatened by the sort of bad weather and poor visibility that forced the cancellation of a similar event on Sunday.
But to the delight of the tens of thousands gathered on The Mall - who had surged forward to get as close to Buckingham Palace as possible - it went ahead as planned.
Queen's procession in open-top carriage procession
Other events during the extended Jubilee weekend included a star-studded concert outside Buckingham Palace on Monday night.
At the end the Queen came on to the stage to press a diamond-shaped crystal into a pod, igniting a beacon in The Mall to mark her 60 years on the throne. It was one of more than 4,000 lit across the UK and the Commonwealth.
On Sunday, about a thousand boats took part in the Diamond Jubilee Thames River Pageant, the first of its kind for 350 years.
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