The 96-year-old died peacefully at Balmoral Castle, her summer home in the Scottish highlands, on September 8.
The certificate, published by the National Records of Scotland on Thursday, records her time of death as 3.10pm (local time).
Buckingham Palace had released a statement just after 12.30pm that day to say doctors were concerned about the Queen's health and that she would remain under medical supervision.
Her death was officially announced at 6.30pm.
She had carried out her last official duty, appointing Liz Truss as Prime Minister - her 15th - just two days earlier.
The Queen, who spent 70 years on the throne, had been suffering from what Buckingham Palace had called "episodic mobility problems" since the end of last year, forcing her to withdraw from nearly all her public engagements.
The certificate shows her death was registered by her daughter, Princess Anne, on September 16.
The Queen has been succeeded by her first son, King Charles III.
She was buried at the royal chapel in Windsor on September 19, featuring a ledger stone bearing her name and those of her parents King George VI and Elizabeth, the Queen Mother, and husband Prince Philip after a state funeral in Westminster Abbey and a service at Windsor.
Prime Minister Jacinda Ardern led a state memorial service for the Queen on Monday, saying the Pacific nation has had "a deep connection" with her as New Zealand paid tribute to the late monarch.
Hundreds watched the service outdoors on the screens set on the Parliament grounds in Wellington as the closed-door ceremony began with a minute of silence at the Cathedral of Saint Paul.
New Zealand is one of 15 countries with the British monarch as the head of state, though the role is largely ceremonial.
