The duchess and her husband enjoyed a carriage procession to the event with other members of the royal family before they all watched the spectacle from Wellington's old office.
"Eugenie and Jack's wedding will be charming and picturesque but it is not an important royal event as she does not undertake royal duties".
Their public appearance together followed media speculation in recent weeks that they had been on honeymoon, although Kensington Palace, Harry's office, has not provided details of any trip.
Andrew took up a more prominent place on the balcony after taking part in his first Trooping the Colour ceremony on horseback in his new role as Colonel of the Grenadier Guards.
Buckingham Palace tweeted that she had only missed one such event during her reign, and that was in 1955 during the country's general strike.
It was also Meghan Markle's first appearance on the balcony with her new family since marrying Prince Harry last month. It originated from traditional preparations for battle when flags, or colors, were "trooped" so soldiers in the ranks would be able to recognize them.
The ceremony has commemorated the birthday of the sovereign for more than 250 years and also functions as a display of army drills, music and horsemanship. Although Queen Elizabeth already turned 92 on April 21, the royals understandably prefer to party and socialize in warmer weather. Since her 2011 Trooping the Colour debut, Kate Middleton has never worn short sleeves, and neither did Princess Diana.
However, it seems as though the Duchess of Sussex is ready to shake up any royal fashion rules, such as the requirement to wear pantyhose.
Prince Philip, who turns 97 today, did not attend the celebrations.
All of the Royal Family was in attendance.
"I'm quite proud and I know that a lot of other people are proud of me as well", he was quoted as saying by the BBC.