A spokesperson said in a statement that it was "It was important to the duke and duchess to be able to personally recognise Remembrance in their own way, to pay tribute to those who have served and to those who gave their lives."
"The couple laid flowers that the duchess picked from their garden at the gravesites of two commonwealth soldiers, one who had served in the Royal Australian Air Force and one from the Royal Canadian Artillery."
According to the statement, they also placed a wreath by an obelisk in the cemetery.
"The duke signed a message with the wreath saying: 'To all of those who have served, and are serving. Thank you'."
It comes after he was reportedly banned from having a wreath laid at a cenotaph on Remembrance Sunday in the UK.
The Duke of Sussex, who was in the British armed forces for 10 years, sent a personal request to Buckingham Palace to have the wreath laid, but was refused as he'd left royal duties in March, reports The Times.
It's thought that the Queen was not informed of the request or its refusal, which has "deeply saddened" Harry.
He spoke about the importance of Remembrance Sunday on a military podcast airing in honour of the event.
On the Declassified podcast, he called the day "a moment for respect and for hope".
"The act of remembering, of remembrance, is a profound act of honour. It's how we preserve the legacies of entire generations and show our gratitude for the sacrifices they made in order for us to be able to live the lives we live today," he said.
In the past, Harry marked the day by visiting the Cenotaph and Westminster Abbey's Field of Remembrance.
Prince Andrew is also not expected to attend the ceremonies in the UK.
Buckingham Palace would not comment on whether Harry's request had been refused, and the duke's own representatives have been contacted for comment.
And during the podcast, Harry spoke about his experiences in the armed forces, describing his relationship with veterans as "like meeting an old mate".
