Marine experts were examining the rare northern bottle-nosed whale to find out more about the mammal whose journey this week was followed by television viewers and thousands of Londoners along the riverbank of the British capital.
The post-mortem results will be published later this week, said Tony Woodley, the director of British Divers Marine Life Rescue (BDMLR) which carried out the last-ditch rescue attempt on the distressed whale.
In a dramatic operation on Saturday covered on live television, marine experts managed to reach the whale that had eluded them after it was first sighted in the river a day earlier, and hoisted it onto a barge before sailing it downriver toward the North Sea.
But the health of the disorientated creature, apparently injured and exhausted, deteriorated over the course of the operation as the barge reached the Thames Estuary, and it died on Saturday evening, about halfway on its journey out to sea.
Costly rescue attempt
The whale, dubbed "Wally" by newspapers which gave it front-page coverage in Britain's Sunday editions, was removed from the barge and is now being examined.
"That post-mortem will go on for most of today," Mr Woodley said.
He said preliminary results would be published in "a joint statement between the Zoological Society of London and BDMLR" on Wednesday or Thursday. More comprehensive results would be available a week or two later.
"Following the post-mortem, the animal will be disposed of by the local authority," Mr Woodley said, adding that health issues would be a major factor in determining whether the public would be allowed to see the lifeless animal.
The BDMLR estimated that the rescue attempt cost them approximately 100,000 pounds (A$236,000).
Though the cause of death was not immediately known, experts had warned that the whale might not be able to cope with the stress of the noise and chaos from crowds and boats around it, as well as the pressure of its own weight on its internal organs.
They also said its lungs and eyes might have been damaged in the fresh water.
The five-to six-metre animal, which weighed between seven and eight tonnes, generated round-the-clock live television coverage and drew popular wonder and sympathy.
It was the first northern bottle-nose spotted in the Thames since records began in 1913.
The whales, pushed close to extinction by commercial whaling until a ban was imposed 25 years ago, are normally found in deep offshore waters in the Arctic Ocean and the northern Atlantic.
Mass media coverage
Newspapers reflected on its tragic demise and what it said about modern Britain.
"Almost the entire nation has spent much of the past two days worrying about the fate of a whale in the Thames," said the Daily Mail.
"Our forefathers would have harpooned the poor creature and cut it to pieces without a second thought. It is a measure of out civilisation that we (now) feel this way," the tabloid wrote.
The Sunday Mirror said: "The care shown by the army of helpers who fought to save the life of Wally, the Thames whale, was human beings at their unselfish best."
People flocked to the Thames riverbanks on Friday to catch a glimpse of the animal, which swam more than 60 kilometres from the open sea and shot spray from its blowhole.
Dolphins, seals and porpoises have all been unexpected visitors to the Thames in recent years, a testament to the recovering state of the once biologically-dead tidal river.
Over the past 30 years, the Thames has improved to become one of the world's cleanest metropolitan rivers.
It might never be known how the whale ended up swimming past London landmarks.
Some experts said it may have become disorientated in the shallow water of the Thames Estuary, or may have been injured by loud sonar used by navy warships in the North Sea.
Reports said a second, larger whale was spotted in the Thames Estuary off Southend-on-Sea, possibly a relative.