The monarch was without her 92-year-old husband Prince Philip, who is spending a second week in hospital recovering from exploratory abdominal surgery.
Kate, who is eight months pregnant, travelled to the Trooping the Colour military parade in a carriage, while William rode on horseback, wearing his uniform as honorary colonel of the Irish Guards, as he did to their wedding in April 2011.
The colourful ceremony is an annual dose of traditional British pageantry, in which soldiers in scarlet tunics and black bearskin hats march in formation.
Catherine rode in an open carriage with William’s brother Prince Harry and the princes’ stepmother, Prince Charles’s wife Camilla.
The heavily pregnant royal smiled and waved to the crowds lining the route to Horse Guards Parade, the central London parade ground.
William and Kate’s first baby, which is due in July, will be third in line to the throne behind William and his father Prince Charles.
Kate carried out her last solo public engagement on Thursday, launching a new liner in the southern English port of Southampton, sending a 15-litre bottle of champagne smashing into its hull.
Prince Edward, the Duke of Kent — a first cousin of the queen — took Prince Philip’s place on the dais to take the salute alongside the sovereign.
The duke, a grandson of king George V who served for two decades in the British army, will be on duty again in a more familiar role within weeks — presenting trophies at the Wimbledon tennis championships.
It is thought to be only the third time that Prince Philip has missed Trooping the Colour after not attending in 1962 and 1968 when he was away on royal tours.
The ceremony — a hangover from preparations for battle when colours or flags were “trooped” down the rank so soldiers could recognise them — marks the queen’s official birthday.
Her actual birthday is on April 21 but traditionally the monarch has another in the summer months, because the weather is supposed to be better for open-air celebrations.
Britain’s only airworthy World War II-era Lancaster bomber was followed by modern Tornado and Typhoon fighter jets.
The Red Arrows aerobatics team then left red, white and blue smoke trailing through the sky.
Despite her husband’s hospitalisation, Queen Elizabeth seemed in good spirits as she waved to the crowds.