The Queen described her Diamond Jubilee celebrations as a "humbling experience" and thanked everyone who had a hand in making them possible.
In a recorded message she said: "It has touched me deeply to see so many thousands of families, neighbours and friends celebrating together".
An estimated one and a half million people filled The Mall earlier in the day to catch a glimpse of the Queen on the balcony of Buckingham Palace.
Prince Philip, the Queen's most constant companion throughout her 60-year reign was notably absent from her side after being admitted to hospital on Sunday with a bladder infection.
The Queen's youngest son the Earl of Wessex said his father was "getting better" after visiting him at the King Edward VII Hospital.
The Queen was joined on the balcony by the Prince of Wales and the Duchess of Cornwall, the Duke and Duchess of Cambridge and Prince Harry.
Despite yet more rain, the planned flypast went ahead, prompting a broad smile from the Queen.
A Dakota flanked by two King Airs, a Lancaster, four Spitfires and a Hurricane from the RAF's Battle of Britain Memorial Flight were followed by the Red Arrows, trailing plumes of red, white and blue smoke.
A Feu de Joie, a fusillade of shots, was then fired by members of the Buckingham Palace Guard of Honour, the 1st Battalion Irish Guard - who then further delighted the Queen with three rousing cheers.
It is only the second time that a feu de joie has been fired in Her Majesty's reign. The first was following the Queen's Birthday Parade in 2006 in celebration of her 80th birthday.
Earlier cheering crowds lined the streets as the Queen's carriage procession travelled through London putting the British pomp and pageantry on full display.
She was joined in her 1902 State Landau for the procession by the Prince of Wales and Duchess of Cornwall.
The Duke and Duchess of Cambridge and Prince Harry rode in a State Landau behind the senior royals and past the cheering crowds.
They had all enjoyed lunch with members of the City of London Livery Companies in Westminster Hall before the spectacle began.
As the carriages emerged from New Palace Yard, near Westminster Hall, spectators began cheering and applauding the 86-year-old Queen.
Their route along Whitehall, through Admiralty Arch and along The Mall was lined by more than 1,000 servicemen and women from the three services.
A 60-gun salute by the King's Troop could be heard in front of Buckingham Palace, and the Queen's Guard awaited her arrival in the palace forecourt.
As the carriage swept in to rapturous applause, the band of the Irish Guards played the national anthem.
The Queen arrived back at the palace through the centre arch. The Prince of Wales and Duchess of Cornwall exited the carriage before the Queen.
The family went through the Grand Entrance where they retired for some private time ahead of their balcony appearance later this afternoon.
The public then flooded onto The Mall in anticipation of seeing the royals on the balcony.
This morning the Queen attended a service of thanksgiving in celebration of her Diamond Jubilee at St Paul's Cathedral.
She was accompanied to the service in a state limousine by one of her ladies in waiting, Diana Marion, The Lady Farnham.
During an extended Bank Holiday weekend, her 60-year reign has been marked by a serious of spectacular national events - a River Thames pageant watched by more than a million people and a music concert last night where a host of famous names performed.
But today the life of the head of the Church of England was being honoured in a religious context through prayers and hymns.
The Queen was joined at the historic cathedral by members of the royal family including the Prince of Wales, Duchess of Cornwall, Duke and Duchess of Cambridge and Prince Harry.
She wore an outfit of fine silk tulle, embroidered with tiny mint green star-shaped flowers embellished with silver thread.
It featured a mint green chiffon drape, scattered with Swarovski crystals on the shoulders. The crown of the hat was covered in the same tulle and was also draped in mint green chiffon and Swarovski crystals.
She was wearing matching drop pearl earrings and necklace, and a brooch on her lapel. The Queen had a black handbag on her arm.
The arrival of the Queen within St Paul's was announced by a new trumpet fanfare written for the occasion and tailor-made for its performance space.
Wing Commander Duncan Stubbs composed the 50-second tune - called Jubilate - and incorporated the cathedral's nine-second echo into the piece.
Waiting close to the cathedral's Great West Door were Charles and Camilla, and William, Kate and Harry, who greeted the Queen.
The service is being conducted by Dr David Ison, the Dean of St Paul's, while while the Archbishop of Canterbury, Dr Rowan Williams, will give the sermon and a special prayer for the Diamond Jubilee will be read.