The Queen was joined by family members including the Prince of Wales and the Duchess of Cornwall, the Duke of Cambridge and the Duke and Duchess of Sussex attended a service at Westminster Abbey before watching the flypast from the balcony of the Palace.
Members of the Royal Family also met veterans, personnel, charity representatives and those from the civil service in a reception after the spectacle.
Air-Vice Marshal Gerry Mayhew, the air officer commanding No 1 group and the senior responsible officer for the flypast, said the day is the "centrepiece" of the RAF's 100th year.
"It is the high point for the capital, Her Majesty the Queen and the royal family," he explained.
"And it is a great opportunity to look back and really celebrate our past, but to look forward is a really important thing for us as we look to the next 100 years."
Chief of the Air Staff, Air Chief Marshal Sir Stephen Hillier, said he hopes the flypast will make the public "proud of their Air Force":
23 different types of aircraft have taken part in the flypast, with nearly 200 aircrew from 25 different RAF squadrons.
The officer commanding 617 squadron, Wing Commander John Butcher, who flew an F-35 during the spectacle, said: "That (Buckingham Palace flypast) will be the first that we will have flown it in a public environment since we landed back, so it is an exciting opportunity.
"Now we just need to make sure the jets are in a good place to fly.
"It is very early days for us, we are still learning to operate back at our main operating base, so there are many factors at play that could prevent us from doing it.
"But, I am still hopeful that we will be able to support it in some way. But the chance obviously still exists that we may not be able to."
It was the first public appearance for the RAF's most advanced war plane since touching down at RAF Marham from the US in June
Helicopters including the Puma, Chinook, Juno and Jupiter also attended.
Aircraft from the Battle of Britain Memorial Flight including the Dakota, Lancaster, Hurricane and Spitfire were part of the line-up, as are training aircraft including the Prefect, Tucano and Hawk.
Helicopters including the Puma, Chinook, Juno and Jupiter are expected to attend.
Aircraft from the Battle of Britain Memorial Flight (BBMF) including the Dakota, Lancaster, Hurricane and Spitfire are part of the line-up, as are training aircraft including the Prefect, Tucano and Hawk.
The Officer Commanding the Battle of Britain Memorial Flight said three Spitfires and two Hurricanes should feature in the flypast.
Squadron leader Andy Millikin said: "It is one of those jobs where even when I was at Coningsby I saw the BBMF - I was a pilot and eligible to go and apply for it, but it never occurred to me that actually it would happen.
"It is one of those dream come true situations, and I still pinch myself every time I go out to fly one of those aeroplanes - it is wonderful."
The Hercules, Atlas A400M, C-17, BAe 146, Sentinel, Voyager, Shadow, Rivet Joint, E-3D Sentry, Tornado GR4 and Typhoon have also taken part.
Drawing the spectacle to a close were the Red Arrows, who in traditional aerobatic style will stream red, white and blue smoke down the length of The Mall.
The flypast began to form up over Suffolk to the west of Ipswich at around 12.45pm, before heading towards Colchester, and then Chelmsford.
The formation continued over the M25, Stapleford Abbotts, Hainault Forest and on to central London - passing the Olympic Park, Hackney, Bethnal Green and Shoreditch before getting to The Mall at around 1pm.
More than £2.4 million of Libor funds grant from the Treasury has been allocated to the RAF to help the celebrate its centenary year, according to Assistant Chief of the Air Staff, Air Vice-Marshal Mike Wigston.
He said: "We got a grant of just over £2 million from the Chancellor which we have been able to use to enhance our local engagement, to do many of the things we wouldn't otherwise be able to do.
"So I have to say the generosity of the Chancellor of the Exchequer with Libor funds has part contributed to the success that RAF 100 is.
"We have got to recognise the good stuff that the Treasury does with these fines - £2.4 million is what we applied for and we have used it."
An RAF spokesman said RAF 100 activity will either be completed within existing resources or funded by a mixture of public funding and £2.43 million from Libor grants from the Treasury.
He added: "All RAF 100 activity costs will be subject to comprehensive scrutiny and audit."
Watch: the history of the RAF in a little over a minute