It was Prince George’s first balcony appearance, which traditionally follows the Trooping the Colour.
It is also the first time Queen Elizabeth has been seen at her birthday celebrations with her heir and heirs apparent.
More than 1,000 soldiers took part in the traditional display of army drill, music and horsemanship.
Twenty three-month old Prince George waved as the Red Arrows took part in a flypast that was largely reduced because of poor weather.
Queen Elizabeth and Duke of Edinburgh earlier travelled by carriage from Buckingham Palace to Horse Guards Parade where the parade took place.
Kate Middleton, meanwhile, made her first public appearance since she left hospital following the birth of Princess Charlotte.
Prince George was earlier pictured in a palace window, from where he appeared to be enjoying the pageantry.
There was no sign of Princess Charlotte but other guests at the event included UK’s PM David Cameron and his wife Samantha.
It is the 63rd time Queen Elizabeth has attended a birthday parade, a record unmatched by any monarch.
Joined by other senior royals, the Queen inspected 1,100 soldiers of the Household Division at Horse Guards Parade.
Earlier, the Prince of Wales, who is Colonel of the Welsh Guards; the Princess Royal, Colonel of the Blues and Royals; and the Duke of Cambridge, Colonel of the Irish Guards, rode on horseback in the procession to Horse Guards.
Kate Middleton, the Duchess of Cornwall and Prince Harry, meanwhile, travelled together to the ceremony in a horse-drawn carriage.
The Duke of York rode in a carriage with his daughters Princesses Beatrice and Eugenie, and the Duke of Kent and the Duke and Duchess of Gloucester were in the final coach.
The Earl and Countess of Wessex are away representing the Queen at the wedding of Prince Carl Philip of Sweden to former reality star Sofia Hellqvist.
The procession was accompanied by a Sovereign’s Escort of the Household Cavalry, made up of Life Guards and Blues and Royals, in their silver and gold breastplates and plumed helmets.
The Color paraded on Horse Guards this year was the flag of the 1st Battalion Welsh Guards.
The Prince of Wales Company, 1st Battalion Welsh Guards, trooped the Queen’s Color presented to them by the monarch at Windsor Castle in April.
The Household Division Bands and Corps of Drums also took part, as are the King’s Troop Royal Horse Artillery who, following the parade, will fire a 41-gun salute in Green Park to mark the Queen’s official birthday.
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