The duke and duchess, who married three weeks ago, made the short trip from Buckingham Palace to Horse Guards Parade in a horse-drawn carriage as royal fans lining the Mall cheered and waved.
After the event, the couple joined other members of the royal family on the palace's front balcony to watch the Royal Air Force fly by.
The 92-year-old queen, who recently had a successful cataract operation, watched the ceremony from a dais and inspected the lines of guardsmen in bearskin hats and scarlet tunics who offered her tributes. Her husband, Prince Philip, has retired from royal duties and did not attend.
The ceremony originated from traditional preparations for battle.
Flags, or colours, were "trooped" so soldiers in the ranks would be able to recognise them.
The Queen's actual birthday is April 21.