The high-profile event on Friday fell on the second day of the national commemorations marking the monarch’s milestone 70 year reign.
The 96-year-old Queen was absent, watching on television from Windsor Castle instead, after she suffered “discomfort” following a busy first day of festivities including a double balcony appearance and a beacon lighting.
It was the first time Harry and Meghan had been on full public view alongside the Windsors since they quit the monarchy for a new life in the US two years ago.
Crowds cheered the pair as they arrived, with the couple smiling and waving at onlookers.
They processed through the nave of the church hand in hand, with Meghan smiling and Harry biting his lip at times.
They were sat in the second row from the front, with Harry next to Princess Eugenie’s husband Jack Brooksbank and Meghan next to Princess Margaret’s daughter Lady Sarah Chatto.
The Sussexes attended the Trooping celebrations at Horse Guards on Thursday, but stayed out of the spotlight inside the Duke of Wellington’s former office with more than 30 members of the family.
More than 2,000 people filled the historic church including Prime Minister Boris Johnson, who was booed by the crowd outside, Cabinet ministers, Labour leader Sir Keir Starmer, first ministers of the devolved governments and every living former prime minister.
Public service is the theme at the heart of the religious event, with 400 people who are recipients of honours, including NHS and key workers who were recognised for their work during the pandemic, invited.
Hundreds of people gathered, some wearing Union flag hats and others hanging flags and bunting over the railings on the approach to the cathedral.
Kate, who was wearing a pale yellow Emilia Wickstead dress and a Philip Treacy hat, walked in the main procession with William, Charles and Camilla.