The light aircraft was carrying the 28-year-old footballer from France to his new Premier League team Cardiff City, when it disappeared near the British island of Guernsey, along with 59-year-old pilot David Ibbotson.
Argentinian footballing idols Diego Maradona and Gabriel Batistuta were among the first to pay tribute to the talented young player, who hailed from the South American country.
The striker's body was spotted by British rescuers using a remotely operated underwater vehicle on Sunday close to where the plane vanished from radar on January 21.
His body was recovered on Wednesday and brought to the Isle of Portland in southern England for formal identification on Thursday by coroners, who investigate deaths in Britain.
"The body brought to Portland Port today has been formally identified... as that of professional footballer Emiliano Sala," police in Dorset, the county where the body was taken, said on Twitter.
"The families of Mr Sala and pilot David Ibbotson have been updated. Our thoughts remain with them all," police said.
- 'Rest in peace warrior' -
Sala's disappearance sparked an outpouring of grief and a flood of cash to support a private hunt for the plane when the official search was initially called off.
"I am very sorry about this sad news. Many of us kept a glimmer of hope for you, Emiliano," footballing superstar Maradona said on Instagram, after the identification of the body.
"What sadness, this is the worst news. Rest in peace warrior," tweeted retired Argentinian football star Gabriel Batistuta.
The country's President Mauricio Macri also offered his condolences to Sala's family following the "painful news". "We are with you," he added.
The small Argentinian town of Progreso, where the footballer lived for most of his childhood, was left "very affected".
"Since we found out, it's all anyone can talk about," said local restaurant owner Oscar Heymo, a friend of Sala's father Horacio. "He was very much loved and admired by all."
- 'Dignified' recovery -
The initial search operations to trace the plane were suspended in the days after it went missing, but a shipwreck hunter hired by Sala's family with funds donated by football stars such as Lionel Messi found the wreckage.
Britain's Air Accidents Investigation Branch (AAIB), then co-ordinated the recovery and the rescued body was taken to Portland Harbour earlier on Thursday and was seen being stretchered into a silver van.
"In challenging conditions, the AAIB and its specialist contractors successfully recovered the body previously seen amidst the wreckage," the AAIB said Wednesday.
"The operation was carried out in as dignified a way as possible."
The crash investigators added that it was unable to recover the plane due to bad weather and as a result has closed down the operation.
The AAIB said that extensive video footage captured of the sunken wreckage is expected to "provide valuable evidence for our safety investigation", adding that it intends to publish an interim report on the accident later this month.
- Private appeal -
The plane, a Piper PA-46 Malibu, vanished from radar around 20 kilometres (12 miles) north of Guernsey, with Ibbotson the only other person aboard.
After the official rescue team gave up their search, saying there was little chance of finding anyone alive, Sala's family raised more than 370,000 euros ($422,000) in an online campaign to pay for a private hunt.
"Had that not happened, I don't think anybody would have searched for the plane," shipwreck hunter David Mearns, whose private company found the plane, told AFP.
The discovery of two seat cushions on the French coast last week revealed that the plane had broken apart, he added.
Sala had been flying in to join up with his new club Cardiff City in what was the most expensive signing in the Welsh club's history.
His former club Nantes have consulted lawyers to explore legal options to ensure Cardiff pay the transfer fee for Sala, a source close to the French club revealed on Wednesday.
According to the source, the first instalment of the 17-million-euro ($19.3 million) deal for the Argentine striker has yet to be paid, despite the transfer being finalised before the accident.
Earlier this week the footballer's father, Horacio, acknowledged that there was no prospect of finding his son alive.
"There's no longer any hope," he told Fox Sports.