"Tenacity, skill and gallantry have been your hallmarks", she said.
The flypast was followed by a solemn rendition of the national anthem, "God Save the Queen", as members of the military formed themselves into the phrase "RAF 100" on the terrace below the palace balcony.
After a spectacular flypast over Buckingham Palace to celebrate 100 years of the RAF, nine jets from the Red Arrows turned the sky red, white and blue over a nursery at Staunton.
Meanwhile, social media pages for the Royal family shared an array of vintage photographs celebrating the family contributing to the RAF throughout its 100 years.More news: How the British media reacted to England's World Cup exit
Queen Elizabeth watched on today as nearly 100 aircraft flew over Buckingham Palace in a celebration to mark the 100th anniversary of Britain's Royal Air Force.
Weather and serviceability dependent, it is expected the new cutting-edge stealth fighter F-35 jets will feature, as well as helicopters including the Puma, Chinook, Juno and Jupiter.
Charles, Camilla, William, Harry and Meghan will also meet veterans, personnel, charity representatives and those from the civil service in a reception after the spectacle.
100 days after the Britain's Royal Air Force (RAF)'s official 100th birthday on April 1, the RAF on Tuesday marked its centenary in a day of national celebrations with the participation of hundreds of aircraft and thousands of people.
She further remembered her father George VI, who became the first member of the Royal Family to qualify as a Royal Air Force pilot.
Donning a fit-and-flare black Dior with a boatneck, not dissimilar from the neckline of her Givenchy wedding dress, Meghan paired it up with a netted hat from Stephen Jones, complementing her elegant side bun which celebrity hairstylists say is fast becoming her signature look since Markle stepped into her royal shoes.