The UK-wide tour was arranged to mark 75 years since the day that Japan ceased fighting on August 15, 1945, marking the end of the Second World War.
The planes were seen soaring over Belfast at around 2.15pm, leaving the famous red, white and blue smoke trails in their wake as it passed the landmark Titanic building and the Harland and Wolff shipyard.
However, due to poor weather, the flypasts over Edinburgh, London and Cardiff were cancelled.
Instead, the Red Arrows flew over Glasgow Prestwick Airport, where the aircraft landed to refuel and meet three Second World War veterans.
The three veterans were 96-year-old Whitson Johnson, Albert Lamond, 94, and 93-year-old Bernard “Barney” Roberts.
Mr Johnson served in the RAF from 1942 to 1947, deciphering codes in support of the Fourteenth Army in the Far East and also spent time in Bombay, Calcutta, Chittagong, Hmawbi and Burma.
Royal Navy serviceman Mr Lamond served from 1943 to 1947 as a signalman.
He fought at Sword Beach during the D-Day campaign and was later attached to the Pacific fleet that joined with the American navy under the command of Admiral Halsey in the Far East.
Mr Roberts also served in the Royal Navy, from 1942 to 1947, initially serving on a minelayer to protect the Arctic convoys from German U-boats before fighting in Italy and North Africa.
In London at around 5.30pm, the Red Arrows are scheduled to fly directly over the Royal Hospital Chelsea, home to three Burma Star recipients, with Chelsea Pensioners to gather in front of the hospital to watch the Hawk jets as they fly overhead.
Also today, a Battle of Britain Memorial Flight planes soared over the nation to commemorate the anniversary.
Spitfires, a Hurricane and a Lancaster Bomber flew over the National Memorial Arboretum in Alrewas, Staffordshire, after Prime Minister Boris Johnson read the Exhortation.
A series of events have been put on to mark the occasion including the televised remembrance service, where a two-minute silence was led by the Prince of Wales and Duchess of Cornwall at 11am.
Richard Day, 93, from Boreham Wood, north London, who was involved in the decisive Battle of Kohima in north-east India, which marked a turning point in the Far East land campaign, was among about 40 veterans at the ceremony of remembrance.
Mr Day, of the Royal Welch Fusiliers, served in the forces which relieved Kohima and Imphal and told of how he contracted malaria and dysentery at the same time, while fighting a highly determined enemy.
He said: “I think the worse part was crossing rivers at night, it was cold at night – then all night in wet clothes and wet equipment, still having to move about.
Unfortunately, the planned flypast of #Cardiff will not be going ahead this afternoon due to the very poor weather conditions in the area. However, the #RedArrows are still expecting to carry out the next scheduled #VJDay75 flypast, which is of #Belfast.— Red Arrows (@rafredarrows)August 15, 2020
“They (the Japanese) were very determined for their emperor.
“It was a glory for them to die for their emperor. They didn’t appear to have any fear at all.”
Charles and the duchess laid poppy posies and wreathes at the Kwai Railway Memorial, while veterans looked on from benches dotted around the memorial, to maintain social distancing.
The prince’s wreath read: “In everlasting remembrance, Charles”, while the duchess’s poppy posy read: “In everlasting remembrance of your service and sacrifice.”
The Covid-19 pandemic has meant tributes to mark the landmark anniversary have been organised online and in television, with the Duke of Cambridge to appear on screens across the country in VJ Day 75: The Nation’s Tribute, a pre-recorded BBC programme filmed at Horse Guards Parade.
Developed with the Ministry of Defence and involving 300 members of Armed Forces personnel, the programme scheduled to broadcast at 8.30pm promises a host of famous faces reading tributes, military bands and dramatic visual projection, with the duke to give a special address thanking veterans and the wartime generation.