The Prince, an RAF Search and Rescue helicopter pilot, made a surprise visit to Camp Bastion in Helmand Province with Defence Secretary Liam Fox, and laid a wreath to commemorate his own friends and others who have lost their lives in war.
The card on William's wreath read: "For Jo, Lex and all those who have made the ultimate sacrifice for our country.
The troops had only learned of the Prince's arrival 15 minutes before he flew in and were delighted to welcome him to their gathering on the parade square.
Sgt Nick Rodgers, from South Yorkshire, serving with Brigade Reconnaissance Force, 16 Air Assault Brigade, said: "Its a big occasion all round. We've got to stay focused for the job in hand but it's still recognised throughout.
"We know that he wants to be here; to be honest, he would rather be out fighting with us so it's good to see him here.
Dr Fox said the service in Bastion had been particularly poignant.
"I think there's a hugely added poignancy to being here because when you're talking about the sacrifices, this is where they are made," he said. "This is where it's at its most raw, its most painful and its most proud.
"There was a very different feel to being here. Prince William and I were very very keen to come here and lend support to our forces when they need it."
In London the Queen led the nation in honouring the fallen.
At the iconic Cenotaph war memorial the monarch was the first to lay a wreath to commemorate those servicemen and women killed in all conflicts since the First World War.
The two minutes' silence began at the first stroke of 11am by Big Ben. The Queen stood metres from the Cenotaph with her eyes fixed on the memorial and her family standing behind her in a line.
The Royal men and women dressed in military uniforms were the Duke of Edinburgh, Prince of Wales, Duke of York, Earl of Wessex, Princess Royal and Duke of Kent, and all stood unmoving as the seconds ticked by.
Close by was Prime Minister David Cameron, Liberal Democrat leader Nick Clegg, opposition leader Ed Miliband, leaders of other parties, High Commissioners from Commonwealth countries and defence chiefs.
Soldiers from the King's Troop Royal Horse Artillery fired a round from nearby Horse Guards Parade which echoed around Whitehall to signal the end of the silence.
As the blast faded Buglers of the Royal Marines sounded the haunting melody of The Last Post, which traditionally signalled the end of a soldier's day.