Prince Philip, who turns 91 next weekend, was taken to hospital with a bladder infection in what the palace said was a "precautionary" move.
He will remain under observation for a few days, meaning he misses the latter stages of the royal festivities, but the monarch still attended Monday's gig featuring pop stars including Paul McCartney, Stevie Wonder and Annie Lennox.
On a clear-skied Monday night, hundreds of thousands of cheering, flag-waving people from around the world packed the grand red road leading to the monarch's 775-room London residence, watching the concert live or on giant screens.
At the end of the three-hour performance, a tired-looking queen took to the stage with her son and heir-to-the-throne Prince Charles who read out a touching tribute.
After thanking the artists and engineers who put the event together, he said: "The only sad thing about this evening is that my father couldn't be here with us because unfortunately he is taken unwell.
"But ladies and gentlemen, if we shout loud enough he might just hear us in hospital," he added, to loud cheers.
The prince sought to sum up the public's affection for a monarch who is seen as a symbol of stability and service at a time of economic gloom and political disillusionment.
"As a nation this is our opportunity to thank you and my father for always being there for us, for inspiring us with your selfless duty and service and for making us proud to be British, proud at a time when I know how many of our fellow countrymen are suffering such hardship and difficulties."
He led a huge, boisterous crowd in three cheers for his mother, and the evening concluded with the national anthem, a spectacular fireworks display and the giant image of a Union Jack flag beamed on to the front of Buckingham Palace.
On Tuesday the queen will be without her husband of 64 years when she attends a thanksgiving service at St Paul's Cathedral, leads a carriage procession through London and waves to well wishers from the balcony of Buckingham Palace.
That gesture will bring to an end four days of nationwide celebrations that climaxed on Sunday when a million people braved heavy rain to watch a 1,000-strong flotilla make its way down the River Thames through the heart of London, led by the queen aboard a gilded royal barge.
At Monday's pop concert, the famous Mall avenue was a sea of red, white and blue, the colours of the Union Jack.
"Being Germans, we would like to be a bit more British!" said Josef Fischer, 60, who travelled with his wife and three children from Bavaria to join the jubilee celebrations.
"On these days you forget everything else. You have fun, you feel good and the troubles come when you go back home."
Robbie Williams opened the show with "Let Me Entertain You", and McCartney ended it with "Let It Be", "Live and Let Die" and "Ob-La-Di, Ob-La-Da" during which he was joined on stage by the other acts.
Wonder sang a jubilee version of "Isn't She Lovely?" before breaking into "Happy Birthday". Veteran crooner Cliff Richard performed a medley of songs, Tom Jones belted out "Delilah" and Shirley Bassey sang "Diamonds Are Forever".
There were classical touches with Lang Lang on piano and Renee Fleming singing opera, and Gary Barlow, who organised the concert, joined a giant choir on stage for a rendition of the song which he and Andrew Lloyd Webber penned for the event.
Elton John was at the piano for "I'm Still Standing", followed by "Your Song" and "Crocodile Rock", prompting a mass singalong that included members of the royal family.
A montage of footage from the queen's 60 years on the throne, including her coronation and silver and golden jubilees, was beamed on to the walls of the imposing palace.
Madness took to the palace roof to perform 1980s hit "Our House", while arguably the highlight of the night was Grace Jones, dressed extravagantly in red and black, keeping a hula hoop spinning around her waist throughout "Slave to the Rhythm".
Affection for queen
The jubilee has underlined the popularity of the 86-year-old queen, head of a royal family which only 15 years ago was mired in scandal after the death of the hugely popular Princess Diana.
The extended holiday weekend celebrations have also been a boon for Britons battered by recession and state spending cuts.
Millions of people have spilled onto streets bedecked in Union Jack bunting up and down the country for outdoor parties during the holiday.
Support is not universal however. Views range from indifference - about two million Britons travelled abroad to benefit from the extra days off - to outright opposition.
"Her achievement is just staying alive, doing little and saying less," Graham Smith, head of campaign group Republic, told Reuters.
And the left-leading Guardian newspaper questioned the long-term future of an ancient institution.
"That the queen is personally admired and revered is not open to doubt ... But is it the monarchy or this particular monarch towards whom these feelings were directed?"
After the concert, the queen lit the last in a network of more than 4,000 beacons burning across Britain and the Commonwealth of mostly former British colonies.
Elizabeth is only the second monarch to mark 60 years on the throne - her great-great-grandmother Queen Victoria reached the milestone in 1897. She is also on course to become the longest-serving British sovereign in 2015.
Her reign began in 1952 and has spanned 12 prime ministers from Winston Churchill to David Cameron.