The Duke of Edinburgh has been taken to hospital with a bladder infection and will miss the rest of the Diamond Jubilee celebrations.
Buckingham Palace said Prince Philip, 90, had been taken to the King Edward VII Hospital in London from Windsor Castle as a "precautionary measure".
The Queen joined 12,000 others at the Jubilee concert at the palace.
The prince will remain in hospital under observation for a few days.
He had appeared to be in good health when he accompanied the Queen on Sunday on the royal barge the Spirit of Chartwell, which formed part of the rain-drenched Jubilee river pageant.
He and the Queen stood for most of the 80-minute journey, as they were accompanied by 1,000 boats travelling seven miles down the river to Tower Bridge.
The prince, who had treatment for a blocked coronary artery in December and turns 91 on Sunday, missed Monday's concert and will not attend the national service of thanksgiving at St Paul's Cathedral on Tuesday.
The Queen, dressed in a black cloak, was helped to her seat by Prince Charles at 21:00 BST, when she joined concert-goers an hour-and-a-half into the celebration.
She ended the concert by pressing a diamond-shaped crystal, igniting a beacon in The Mall marking her 60 years on the throne.
Other beacons had earlier been lit across the UK and the Commonwealth.
Robbie Williams - who earlier opened the show with Let Me Entertain You following a firework display and an Armed Forces fanfare - was the first to perform for the Queen when he sang big band classic Mack the Knife.
Other performers included Jessie J, Annie Lennox, Sir Tom Jones, Madness, Stevie Wonder and Sir Cliff Richard - singing a medley of his songs from six different decades.
Comedians including Lee Mack, Rob Brydon, Jimmy Carr and Peter Kay - dressed as a Beefeater - also performed at the event which was broadcast by the BBC.
Performers from around the Commonwealth collaborated on Sing, a piece co-written for the occasion by Gary Barlow and Lord Lloyd Webber.
The concert was brought to a close by Sir Paul McCartney who played hits including Magical Mystery Tour, Let It Be and a spectacular rendition of Live and Let Die, complete with fireworks and explosions.
He was joined on stage at the end by all of the night's performers for The Beatles' Ob-La-Di, Ob-La-Da.
The Queen and other members of the Royal Family also made their way onto the stage where Prince Charles paid tribute to his mother.
"Your majesty, mummy," he began before thanking "all the wonderful people that made tonight possible".
"And if I may say so, your majesty, thank God the weather turned out fine," he added.
"And the reason, of course, is because I didn't do the forecast," he said, referring to his recent foray into weather presenting, in a special BBC broadcast.
"The only sad thing about this evening is that my father couldn't be with us because, unfortunately, he was taken ill but if we shout loud enough he might hear us in hospital," he concluded.
Turning to his mother, he said: "As a nation, this is our opportunity to thank you and my father for always being there for us, inspiring us with your selfless duty and service and for making us proud to be British."
The Queen then lit the final one of 4,500 beacons across the world marking her 60-year reign.
She placed a crystal glass diamond into a special pod, triggering the lighting of the Jubilee beacon in The Mall with its 6m-high flame.
In an enclosure at the front of the stage were many invited guests including Emily Lewis, from Barnado's in Cardiff, who brought four children with learning difficulties to see the show.
One of the youngsters, Jenny, said she was most excited about seeing boy band JLS.
"I feel really lucky, I'm enjoying it," she said.
The Duke and Duchess of Cambridge and Prince Harry - who all sang along to songs including Elton John's Crocodile Rock - were in the audience as were politicians including Prime Minister David Cameron and Deputy Prime Minister Nick Clegg.
Thousands without tickets watched the concert on The Mall nearby.
Samuel Mellows, 20, from Poole, Dorset, was at the front of The Mall crowd all day - though he was less easy to spot since he took his union jack top hat off so others behind him could see.
"What a way to start the gig with Robbie Williams," he said.
"It was phenomenal. I got goose bumps and they haven't stopped - what a way to celebrate such a wonderful woman."
The St Paul's service was due to be followed by two receptions, a lunch at Westminster Hall and a carriage procession to Buckingham Palace, with a balcony appearance by the Queen and a fly-past.
A palace spokesman said the prince was "understandably, disappointed about missing this evening's Diamond Jubilee Concert and tomorrow's engagements".
Caroline Couzens, 54, a hospice worker from Dorchester in Dorset, was among those on The Mall who heard about the prince falling ill.
She said: "I think people will still enjoy the party but obviously it will put a dampener on things for the royals. It's very sad he won't be there."
Barry Cramner, from Bournemouth, was one of those taking part in a special picnic in the gardens of Buckingham Palace.
He told the BBC: "It's a great shame for the Queen and not the way she would have wanted to finish the weekend. Our thoughts go out to her."
Take That star Gary Barlow, who helped organise much of the concert and sang a duet with Cheryl Cole, said the prince's illness was "sad, really sad".
Ahead of the the concert, Sir Paul said: "I hope he's okay."
"We all send our best wishes for a speedy recovery - I hear it's not too bad."
Beacons were lit in Commonwealth countries including Tonga and Australia.
They were ignited at 22:00 local time in the Commonwealth and British overseas territories - those in the UK, Channel Islands and Isle of Man were be set alight between 22:00 and 22:30 BST.
Beacons were placed on the battlements of the Tower of London, and at St James's Palace, Lambeth Palace, Windsor Castle, Sandringham, Balmoral and Holyrood House and on Hadrian's Wall.
Fires on the highest peaks of the UK's four nations - Ben Nevis, Snowdon, Scafell Pike and Slieve Donard - were lit up by teams from four charities.
A beacon was also lit at the hotel in Kenya where the Queen was told in 1952 of her father George VI's death.
Ticket-holders for the star-studded Diamond Jubilee concert also attended a picnic at Buckingham Palace.
They entered the palace gardens - where teams of helpers handed out picnic hampers created by celebrity chef Heston Blumenthal and royal chef Mark Flanagan - to the accompaniment of a steel band.
Some 10,000 winners of a public ballot and 2,000 VIPs are at the palace for the picnic and concert.
Thousands of people also watched the concert on big screens in St James's Park, Hyde Park and Trafalgar Square.
The Diamond Jubilee Concert was shown on BBC big screens in 22 towns and cities throughout the UK.
See all the latest Diamond Jubilee news and features at bbc.co.uk/diamondjubilee