The couple marked the occasion from the United States, hours after much of Britain's Royal Family gathered in Central London for the annual service at the Cenotaph war memorial.
Remembrance Sunday, the Sunday closest to November 11, is the day the UK pays tribute to those who lost their lives in war.
The couple laid flowers that the Duchess picked from their garden at the graves of two Commonwealth soldiers, one who had served in the Royal Australian Air Force and one from the Royal Canadian Artillery, a spokesperson for the couple said.
Both Harry and Meghan wore poppies, a symbol of remembrance in the UK and across much of the Commonwealth, while Harry also wore military medals across his suit.
Meghan and Harry, who spent 10 years in the armed forces and undertook two tours of Afghanistan, wanted to be able to personally recognize Remembrance Day in their own way, their spokesperson added.
The Duke and Duchess also placed a wreath at an obelisk in the cemetery that is inscribed: "In Memory of the Men Who Offered Their Lives in Defense of Their Country."
The Duke signed a message with the wreath saying: "To all of those who have served, and are serving. Thank you."
Harry also gave an interview to the Declassified military community podcast, saying "even when we can't be together, we remember together."
The couple removed their face masks when on their own or at a distance from others, the spokesperson added.
Earlier this week, Britain's Queen Elizabeth II wore a face mask for the first time while appearing in public during the pandemic, at a commemorative ceremony ahead of Remembrance Sunday.
Meanwhile, in London on Sunday, Harry's family, including his father, Prince Charles, and brother, Prince William, laid wreaths at the Cenotaph. The event was pared back due to Covid-19 restrictions.
The socially distanced event was preceded by a two-minute silence and was observed by the Queen from the balcony of the Foreign Office.