A total of 33 Spitfires, Hurricanes and Bristol Blenheim bombers flew from Goodwood Aerodrome in West Sussex before dispersing across wartime airfields over the south of England for the event to mark the conflict’s 75th anniversary.
The prince, on his 31st birthday, was due to have a seat in one of four two-seater Spitfires taking part in the flypast but when one of the vintage aircraft developed mechanical problems he decided to step aside to ensure the event’s special guests would still get to fly.
His spokesman said he wanted to make sure that 95-year-old Tom Neil, a former wing commander and Battle of Britain Hurricane and Spitfire pilot, would still be able to take part.
And he wanted to ensure that a former para and an RAF corporal who won places on a Spitfire scholarship training programme were also still able to take part in the display.
Nathan Forster, a former private in the Parachute Regiment, from South Shields, suffered severe damage to his left leg in an IED blast while on patrol in Afghanistan in 2011.
Corporal Alan Robinson, an RAF aircraft technician, from Market Rasen, Lincolnshire, lost a leg in a motorbike accident.
The prince’s spokesman said: “Prince Harry wanted to make sure they could take part in the flypast. It’s a case of counting them out and counting them in.”
Harry took the chance to wish Mr Forster well as he took the prince’s seat in the Spitfire PV202. After waving him off, Harry took a mobile phone photograph of the plane before it manoeuvred on to the runway.
As the prince watched the Spitfire take off, a group of schoolchildren sang Happy Birthday and he waved back. During the display, Harry took photographs and video on his mobile phone and clapped as the aircraft flew past.
The scholarship was established by the Boultbee Flight Academy and is supported by the Royal Foundation of The Duke and Duchess of Cambridge and Prince Harry’s Endeavour Fund – which donates money and offers practical help to sporting and adventure challenges for wounded ex-service personnel.
Harry had been due to fly in the Spitfire PV202 piloted by John Romain, managing director of the Aircraft Restoration Company at Duxford, Cambridgeshire.
But the prince has previously been able to fly in a Spitfire when he met pilots in August last year who were training for the event.
The display, which had been delayed by two hours because of poor weather, is a tribute to the Second World War pilots famously dubbed “The Few” by wartime prime minister Winston Churchill for their efforts defeating the Luftwaffe.
During the summer and autumn of 1940, 544 personnel from Fighter Command died as the RAF fought in the skies above southern England to force back the threat of any invasion by Hitler.
The 75th anniversary is likely to be the last at which the surviving members of the conflict – who are now all aged well into their 90s – will be fit to take part.
The event has been organised by the Boultbee Flight Academy, based in Chichester, and two of the aircraft – a Spitfire and a Hurricane – fought in the famous battle.
After Mr Neil landed, he said from the cockpit: “It was delightful.”
He added: “It was nice to be back in a Spitfire again.” Of the prince, he said: “He’s a lovely, lovely man, he welcomed me back, we had been talking about it at dinner last night, he was so keen, so welcoming.”