Wearing a black face mask she arrived at St George’s Chapel in a Bentley, to remember her husband of 73 years.
Due to strict coronavirus restrictions the monarch was forced to sit through the 50 minute service by herself.
Prince Charles had tears in his eyes as he walked behind his father’s casket which had been draped in the duke’s own personal standard and topped with a sword, a naval cap and a wreath of flowers.
Although only 30 members of the Royal Family were allowed inside the church, 730 members of the armed forces took part in the event.
Following a national minute’s silence at 3pm the service was carried out by the Dean of Windsor David Conner and the Archbishop of Canterbury Justin Welby.
There was no sermon and no eulogy in line with the duke’s wishes.
Philip’s life and legacy were remembered during the ceremony which reflected on his naval career, passion for engineering and dedication to the Queen.
The duke was described as enriching the lives of all those he knew with his “kindness, humour and humanity”.
The Dean of Windsor said Philip’s life had been “a blessing”.
“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,” he said.
“Our lives have been enriched through the challenges that he has set us, the encouragement that he has given us, his kindness, humour and humanity.”
The duke’s coffin was transported to the chapel in a customised Land Rover as senior members of the Royal Family followed.
Princes William and Harry did not walk shoulder to shoulder during the procession but did sit opposite each other during the service.
When they left the chapel the brothers were seen engaging in a private conversation.
After the ceremony the duke’s coffin was lowered into the Royal Vault of St George’s Chapel by electric motor.
The service follows precise instructions left by Philip who died peacefully eight days ago at the age of 99.
Philip’s death left the monarchy grieving in private, but they made public appearances to recognise the support and condolences they received throughout the week from the nation.
Charles spoke first for the family and praised his “dear Papa” for the “most remarkable, devoted service to the Queen, to my family and to the country”.
A few days later he understandably looked more emotional when he saw first-hand at Marlborough House the hundreds of cards, flowers, letters and pictures left by the public wanting to honour his father.
Personal, funny and revealing tributes were paid by the duke’s children and grandchildren who knew him best, and saw a side of the duke only glimpsed at by the outside world.
The Duke of Sussex summed up his “grandpa” as “master of the barbecue, legend of banter, and cheeky right till the end” while the Duke of Cambridge pledged to uphold his wishes and continue to support the Queen and “get on with the job”.
Unseen photographs were released showing Philip sitting on a sofa with the Queen at Balmoral surrounded by their great-grandchildren, having a bite to eat with his family with a beer at hand or in the Scottish Highlands relaxing with his wife.