Sala, 28, was travelling to Cardiff in a plane piloted by David Ibbotson, which went missing over the English Channel on 21 January.
The Argentine’s body was recovered late on Wednesday after the wreckage was found on Sunday morning.
Dorset Police confirmed the identification on Thursday night.
In a statement, the force said: “The body brought to Portland Port today, Thursday 7 February 2019, has been formally identified by HM Coroner for Dorset as that of professional footballer Emiliano Sala.
The body was spotted in the wreckage of the plane on Monday and the authorities were able to recover it two days later, despite “challenging conditions”.
The Air Accidents Investigations Branch (AAIB) said the operation had been carried out in “as dignified a way as possible” and the men’s families were kept updated throughout.
The Geo Ocean III, which was involved in finding the wreckage, took the body back to the nearest port of Portland in Dorset, where the body was formally identified.
The Piper Malibu N264DB was en route from France to Cardiff, after the Argentine striker made a quick trip back to his former club Nantes two days after his £15m transfer to Cardiff was announced.
Cardiff City issued a statement shortly after identification was confirmed saying: “We offer our most heartfelt sympathies and condolences to the family of Emiliano. He and David will forever remain in our thoughts.”
Some of the club’s players reacted via Twitter. Full back Joe Bennett wrote “RIP Emiliano”, while centre-half Sol Bamba posted a black-and-white image of the team-mate he never got to play alongside.
Stars from the wider footballing world also paid tribute.
Chelsea defender Antonio Rudiger wrote: “Heartbreaking to hear the news about Emiliano Sala. Rest in peace! Thoughts go out to the family and friends of Emiliano and the pilot.”
And Arsenal’s Mesut Ozil tweeted: “No words to describe how sad this is. Thoughts and prayers go out to his family and also to the family of the pilot.”
Mr Ibbotson, 59, from Crowle, North Lincolnshire, was at the controls when the flight lost contact with air traffic controllers on 21 January.
Tragic… May you rest in peace. ❤️ pic.twitter.com/ybrax86w1t
— Sol Bamba (@Sol14Bamba) February 7, 2019
He is yet to be found.
An official search was called off on 24 January after Guernsey’s harbour master said the chances of survival were “extremely remote”.
But an online appeal started by Sala’s agent raised £324,000 (371,000 euros) for a private search led by marine scientist and oceanographer David Mearns.
Working jointly with the AAIB, his ship and the Geo Ocean III, began combing a four square mile area of the English Channel, 24 nautical miles north of Guernsey, to make best use of the available sensors.
Enorme tristeza 😢 QEDP Emiliano. Mis condolencias a familiares y amigos #PrayForSala 🙏🏾//Terribly sad 😢 Rest in peace, Emiliano. My condolences to his friends and family #PrayForSala 🙏🏽 pic.twitter.com/n9aV5CGcI1
— Sergio Kun Aguero (@aguerosergiokun) February 8, 2019
Mr Mearns said the plane was identified by sonar, 67m (220ft) below the surface, before a submersible with cameras was sent underwater to confirm this.
Following the confirmation, he also tweeted his tribute.
“I was glad to provide some small comfort to Romina, Mercedes and the whole Sala family during the past two weeks but my heart goes out to the family and friends of David Ibbotson whose loss is the same,” Mr Mearns said.
During the recovery operation, the AAIB used a remotely operated underwater vehicle (ROV) to aid the search, with no divers involved.
The body was moved first, and separately from the wreckage, to maximise the chances of it being successfully brought to the surface.
It said efforts to recover the crashed plane as a whole proved unsuccessful, before being abandoned due to poor weather.
“The weather forecast is poor for the foreseeable future and so the difficult decision was taken to bring the overall operation to a close,” the AAIB said in a statement.
However, the AAIB said video footage captured by the ROV would provide “valuable evidence” for its safety investigation.
Mr Mearns told BBC Radio Wales the AAIB could not have continued searching in the current conditions and admitted finding Mr Ibbotson’s would be difficult.
He added: “I’ve been involved in operations when people were lost and the bodies were found days and weeks after, not far from where they were lost.
“But this is a pretty dynamic place. It’s got fairly strong currents, it’s not that deep water, you’ve got a lot of fishing activity, a lot of scallop dredgers moving in and out of the location.
“You cannot expect that the body is going to be in that location for an extended period of time.”
Sala was Cardiff’s record signing but never played for the club.
The fee was due to be paid over three years but Cardiff have withheld the first scheduled payment until they are satisfied with the documentation.