This will be the first time since 1963 that the Queen will have missed this constitutional ceremony, which sets out the government's legislative plans.
Prince Charles will deliver the speech on Tuesday for the Queen.
The 96-year-old monarch has mobility problems and has had to cancel a number of recent public appearances.
Until Monday evening Buckingham Palace had been saying the Queen hoped to attend, but has now confirmed she will not go the ceremony in Westminster, because of "episodic mobility problems".
A statement said the Queen, in consultation with her doctors, had reluctantly decided not to attend the State Opening.
It follows the Queen missing events at Easter, including the Maundy Service, and the announcement that she would not host royal garden parties this year.
The thanksgiving service for Prince Philip in March has been the only public event outside of her royal residences that she has attended so far this year.
The State Opening of Parliament marks the start of the parliamentary year, with the Queen's speech setting out the agenda of the government and the laws that it wants to introduce.
The speech is usually read out by the monarch, as head of state, with the Queen only missing it twice during her 70-year reign, in 1959 and 1963, because of pregnancies.
On those occasions the speech was delivered by the Lord Chancellor, but the Prince of Wales will stand in for the Queen this year.
There have been adaptations of the State Opening in recent years - with the Queen not wearing the heavy Imperial State Crown or ceremonial robes and there was a more scaled-back ceremony last year because of Covid restrictions.
But this will mark the first time in 59 years that the Queen will not have attended.