Elizabeth, dressed in black and in a white trimmed black mask, stood alone as the funeral service began in St George's Chapel.
Mourners at the ceremony in Windsor Castle, including Prince Charles and his sons Princes William and Harry, were restricted to just 30 and separated due to COVID-19 rules. Prince William and Harry walked into the chapel separately.
"We are here today in St George's Chapel to commit into the hands of God the soul of his servant Prince Philip, Duke of Edinburgh," the Dean of Windsor, David Conner, said.
"We have been inspired by his unwavering loyalty to our Queen, by his service to the Nation and the Commonwealth, by his courage, fortitude and faith."
After the nation observed a minute's silence in brilliant sunshine, Harry and William took up their places on opposite sides of the chapel with the final resting place of Tudor monarch Henry VIII dividing them.
The entire funeral was televised live to allow the citizens of the UK to grieve for Prince Philip following his death last week at the age of 99. Meghan Markle watched the funeral at her home in California after she was advised by her doctor not to travel while pregnant.
Earlier the Queen has left Windsor Castle to attend the funeral of her “beloved” husband the Duke of Edinburgh.
It is the first time she has been officially seen in public since she announced Philip died peacefully last Friday morning at Windsor.
The national anthem was played by military musicians after the Queen, joined by a Lady-in-Waiting, left the Sovereign’s entrance.
A Bentley carrying the head of state and her Lady-in-Waiting took up its place at the back of the funeral procession.
The Queen led a small group of close family and friends at the service for her husband of 73 years.
Covid regulations reduced the scope of the service with public elements cancelled, mourners reduced from around 800 to just 30 and all guests wore face masks and sat apart.
The duke’s coffin could be seen draped with his personal standard, which pays tribute to his birth heritage as a Prince of Greece and Denmark, his family name and his Edinburgh title.
Philip was made the Duke of Edinburgh shortly before his wedding in 1947, by his future father-in-law George VI.
Philip’s custom-built Land Rover Defender hearse, designed by the duke and modified over 16 years, was driven into the castle’s quadrangle and has stopped outside the Equerries’ entrance.
The Defender TD5 130 chassis cab vehicle was made at Land Rover’s factory in Solihull in 2003, the year he turned 82.
With its heavy-duty wheels and angular structure, the polished sturdy, utilitarian vehicle stands as a showcase for the duke’s practical nature and his passion for functional design and engineering.
Chief of the Defence Staff General Sir Nicholas Carter, who is head of UK Armed Forces, along with the heads of the Army, RAF and Royal Navy, walked from the Equerries’ entrance and took up positions by the State entrance and faced the Land Rover.
"She's the queen, she will behave with the extraordinary dignity and extraordinary courage that she always does. And at the same time, she is saying farewell to someone to whom she was married for 73 years," said Justin Welby, the Archbishop of Canterbury, who will help officiate at the service.
Philip, who married Elizabeth in 1947, helped the young queen adapt the monarchy to the changing world of the post-World War Two era as the loss of empire and the decline of deference challenged the world's most prominent royal family.
She has now been widowed just as she grapples with one of the gravest crises to hit the royal family in decades - allegations of racism and neglect by it from her grandson Harry and his American-born wife Meghan.
Much media attention will focus on the royals' behaviour towards Harry as he made his first public appearance with the family since the couple gave an explosive interview to Oprah Winfrey last month.
In the interview they accused one unnamed royal of making a racist comment, and said Meghan's pleas for help when she felt suicidal were ignored.
The couple, who moved to Los Angeles and quit royal duties last year, laid bare their perceptions of the family's attitudes in what amounted to a critique of the old-fashioned customs of an ancient institution.
Meghan said she had been silenced by "the Firm" while Harry said his father, Charles, had refused to take his calls. Harry said both Charles and his brother William were trapped in the royal family.
Meghan, who is pregnant, did not attend Saturday's funeral as her doctor has advised against it, Buckingham Palace said.
Mourners ditched the tradition of wearing military uniforms, a step newspapers said was to prevent embarrassment to Harry, who despite serving two tours in Afghanistan during his army career, is not entitled to wear a uniform because he was stripped of his honorary military titles.
"We're not going to be drawn into those perceptions of drama, or anything like that," a Buckingham Palace spokesman said. "This is a funeral. The arrangements have been agreed, and they represent her majesty's wishes."
Prince Andrew, who stepped down from public duties in 2019 over controversy surrounding what he termed his "ill-judged" association with late US financier Jeffrey Epstein, had wanted to wear an admiral's uniform at the funeral, British media reported.
The palace had emphasised that while the occasion will have the due pageantry that marks the passing of a senior royal, it remains an occasion for a mourning family to mark the passing of a husband, father, grandfather and great-grandfather.
There was just 30 mourners inside the chapel for the service because of Covid-19 restrictions.
Philip's dedication to his duty earned him widespread popularity in Britain, but he was also criticised by some for a number of off-the-cuff racist or abrupt comments which shocked princes, priests and presidents.
"He was authentically himself, with a seriously sharp wit, and could hold the attention of any room due to his charm and also because you never knew what he might say next," Harry said of his grandfather.
British television stations have cleared their schedules to show the funeral and millions are due to watch, though there have been over 100,000 complaints to the British Broadcasting Corporation over its blanket coverage since Philip died.
Philip was a decorated Royal Navy veteran of World War Two and his funeral, much of which was planned in meticulous detail by the prince himself, will have a strong military feel, with personnel from across the armed forces playing prominent roles.