The monarch -- who was crowned June 2, 1953 -- turned 92 on April 21.
This marks the first time Harry and Markle have attended the annual function together. They were married on May 19.
Also seen participating in this weekend's military parade and watching the Royal Air Force flyby demonstration were Harry's father Prince Charles, his brother Prince William, sister-in-law Kate Middleton, niece Princess Charlotte, nephew Prince George and other members of the royal family.
People magazine reported Middleton was seen comforting tearful 3-year-old Charlotte after she lost her balance and fell while watching planes fly by with her family on the terrace of Buckingham Palace.
Field Marshal Lord Guthrie, the 79-year-old former head of the army and chief of defense staff, fell from his horse during the parade and was taken to the hospital, the BBC said.
His condition was not immediately known.