They gathered at the Franco American-led remembrance service set amidst the graves of thousands of dead US servicemen in Colleville-sur-Mer in Normandy, France.
Mr Brown put aside the political turmoil of a chaotic cabinet reshuffle and spate of resignations to represent Britain's role in ensuring June 6, 1944 became the greatest military victory in history.
But France has been heavily criticised for its Franco-American focus for the 65th anniversary, overshadowing the important role played by British and Canadian forces.
The Prince's last-minute visit was hastily arranged following claims the Queen had been snubbed by the French.
The Union flag was notably absent from the ceremonial ground at Colleville., which was dominated by the flags of France and the US. But standard bearers carried the Allies' flags, which included the Union flag.
Thousands of war graves were instead decorated with both a French and US flag with the symbol of the two nations also flying at full mast above the ceremony.
A documentary about the deadly invasion played to the thousands of guests before the ceremony adopted a distinctly US slant focusing on the American casualties, memorials and the US struggle to advance the front line.
Little mention was made of the British servicemen and military chiefs who played key roles and lost their lives in the Normandy campaign.
Mr Brown and the Prince had earlier attended a remembrance service at Bayeux Cathedral.
They smiled and chatted after taking their seats.
During the service Mr Brown seemed agitated, constantly fidgeting in his seat.
His wife Sarah, wearing a brown checked dress, accompanied the Prime Minister to the event, organised by the Royal British Legion.
Bob Ainsworth, appointed Defence Secretary yesterday after the resignation of John Hutton, also joined the service which Mr Hutton had been due to attend.
Chief of the Defence Staff Sir Jock Stirrup and French Prime Minister Francois Fillon were also present for the service, which saw the 13th century Norman Gothic church filled with Normandy veterans, serving servicemen and women and sea, Army and air cadets.
The Prince was the first to lay a wreath. The circle of poppies with white carnations forming a fleur de lys - the Prince's emblem - bore the message: "In grateful and everlasting memory - Charles."
Mr Brown also laid a wreath in the cathedral, which was followed by a floral tribute from Mr Fillon.
The service was accompanied by music from The King's Division Band.
Afterwards the Prince, Mr Ainsworth, Sir Jock and Mr Fillon travelled to nearby Bayeux cemetery where the Normandy Veterans Association held a moving service among the graves of fallen British soldiers who gave their lives during the campaign to free Europe from Nazi occupation.
Mr Brown was not able to attend as he was hosting a reception for veterans at a hotel in Bayeux.
Hundreds of Normandy veterans paraded into the cemetery to remember the bravery and sacrifice of the troops who landed in northern France from June 6, 1944 onwards.
Thousands of family, friends and well-wishers from Britain, France and other European countries applauded them as the men marched in the warm sunshine.
Children from St Joseph's School, in Hendon, north London, also greeted the veterans with signs saying "The Young Do Care" and "Thank you".
The day, which had started with cloudy skies, was so warm by the time the service began that one standard bearer fainted and had to be carried away for treatment.
The Prince and Mr Fillon were among those who laid dozens of wreaths as the service remembered those who gave their lives in the name of freedom.
The crowds formed a circle with some standing among the graves, several veterans resting a hand on top of the headstones as if to include their lost colleagues in the event.
During the service, the many cadets present pledged to continue remembering D-Day when the veterans themselves were unable to continue making the pilgrimage to Normandy.
The service also included a prayer for the troops currently serving the Queen.
After the service, the Prince spent about 30 minutes meeting veterans and cadets who cheered and clapped him as he walked around the cemetery.
Many said they were thrilled he had attended after the French authorities failed to invite the Queen.
Peter Lennard, a troop commander with 30th Corps Anti Tank Regiment on D-Day, said afterwards: "It was lovely to meet him.
"I was so fed up about it. I felt like saying to him 'how's your mum?"'
Mr Lennard, 92, from Maidstone, Kent, was on the first assault on D-Day, landing on Sword Beach at 7.15am.
Today he used a mobility scooter although he stood to meet the Prince, and said: "I arrived in a tank and I'm going in a scooter."
Frederick Wright, 88, of Beccles, Suffolk, was in a wheelchair and said he had apologised to the Prince for being unable to stand up to greet him.
He was a sapper with 7th Armoured Division and spent much of D-Day waiting on a boat watching the smoke and explosions come up from the beaches. He later landed at Gold Beach.
Major General Tony Richardson, the president of the Normandy Veterans Association who served with the 147th Essex Yeomanry on D-Day, said today's service had been "absolutely tremendous".
"The Prince of Wales is terrific. He managed to speak to so many people, so many veterans and shook so many hands.
"It's wonderful to see so many veterans here. We are getting a little bit older but we remember everything that happened 65 years ago even if we have difficulty remembering what happened yesterday."
Mr Obama looked relaxed as he and his wife Michelle, dressed in white dress and jacket with a gold belt, arrived in Colleville by helicopter to a brass band playing a composition of rousing 1940s military music.
Mr Sarkozy was accompanied by his wife Carla Bruni Sarkozy wearing a white short-sleeved dress, black jacket and matching belt.
Mr Brown sang along as God Save the Queen was amongst national anthems played to the thousands gathered in front of the open arc memorial with its 22 foot bronze statue, The Spirit of American Youth Rising From The Waves.
A total of 9,387 US servicemen are buried at Colleville's American Cemetery, 307 whose names are unknown.
Their resting place overlooks Omaha beach, the last and toughest beach to capture on D-Day.
Actor Tom Hanks, who played Captain John H Miller in the film Saving Private Ryan which dramatises the horror of the Omaha landing in its opening sequence, was amongst guests.
The film's director Steven Spielberg was also invited to attend.
Mr Brown said: "65 years ago in the thin light of grey dawn more than 1,000 small craft took to a rough sea on a day that will be forever a day of bravery.
"On that June morning the young of our nations stepped out on those beaches below and into history.
"As long as freedom lives their debts will never die."
He added: "On D-Day the sounds of liberation on the march were heard across Europe."
Mr Brown said it was an "honour" to speak for the British people on this day which marks the "triumph of right over wrong, truth over lies".
He said Europe and America were allies "not for a season but for centuries" and added: "In June 1944 in this place and at that moment Europe and America came closer together than at any time and any country."
Mr Brown praised British veteran Jack Woods who was presented with the rank of Officer of the Legion d'Honneur, France's highest military distinction, by President Sarkozy during the ceremony.
He said: "I know the whole of Britain will be proud that their veteran is today decorated by President Sarkozy."
He spoke of trouble in Darfur, Burma, Zimbabwe and of poverty and hunger and the legacy of the Second World War.
"How can we say we have achieved all that we set out to do. The promise of peace and justice?" he said.
"There are dreams of liberation still to be realised, commitments still to be redeemed.
"We must be liberators for our generation."
He added: "The beacon of hope that was lit and the liberation of Europe must now lead us on."
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