The couple are in the process of divorcing after 12 years of marriage and will share custody of their daughters, nine-year-old Savannah and seven-year-old Isla.
The announcement comes a month after Peter, son of Princess Anne, attracted criticism for starring in a Chinese advert for a milk company.
A spokesman for the couple said they had informed the Queen and their families of the decision last year.
The statement said: “The decision to divorce and share custody came about after many months of discussions and although sad, is an amicable one.
“Both families were fully supportive of Peter and Autumn in their joint decision to co-parent. Their first priority will remain the continued wellbeing and upbringing of their daughters.
“Both Peter and Autumn have remained in Gloucestershire to bring up their two children. They have requested privacy and compassion while the family continues to adapt to these changes.”
Autumn, 41, was born in Canada and met Peter, 42, during the 2003 Montreal Grand Prix, where they were both working.
She said she did not realise he was the Queen’s grandson until six weeks into their relationship.
Brought up Roman Catholic, she renounced her faith shortly before their wedding so her husband-to-be could retain his place in the succession — currently 15th in line to the throne.
The couple tied the knot at St George's Chapel, Windsor Castle, in 2008, but courted controversy when they sold their wedding photos to Hello! magazine for a reported £500,000.
The separation is the latest in a series of setbacks for the Queen and royal family.
It comes after the Duke of York stepped down from royal duties amid the Jeffrey Epstein scandal, and the Duke and Duchess of Sussex decided to move to Canada.