Russia's Investigation Committee said the results of genetic tests had established the identities of the 10 people who died in a plane crash last Wednesday, including the mercenary group founder.
He had been listed as a passenger on the plane that crashed near Tver, 180km north-west of Moscow, two months after the group mounted a mutiny against the Russian military.
Earlier this week, Russia’s civil aviation authority said Mr Prigozhin, along with some of his top lieutenants, were on the list of those on board the plane that crashed Wednesday.
The investigations committee confirmed the bodies recovered from the site “conformed with the flight manifest”.
Mr Prigozhin, 62, led a failed mutiny against Moscow exactly two months before the crash.
Fighters from the mercenary group came within 200km of Moscow in a move slammed as treason by President Vladimir Putin.
The president quickly exiled Mr Prigozhin, once a top confidant, to Belarus.
He has now ordered Wagner fighters to sign an oath of allegiance to the Russian state after the death of Mr Prigozhin.
Mr Putin signed the decree bringing in the change with immediate effect on Friday after the Kremlin said that Western suggestions that Prigozhin had been killed on its orders were an “absolute lie.”
On Thursday, Mr Putin said he had known Prigozhin since the early 1990s, and described him as a "talented businessman" but also as a flawed character who "made serious mistakes in life".
They were both born in St. Petersburg. From a hot dog stand, Mr Prigozhin built a catering company and owned several high-end restaurants, and became known as 'Putin's chef'.
But he was to rise to far greater prominence as the head of the mercenary group, Wagner.
Wagner fighters played a prominent role in the conflict in eastern Ukraine, especially during the months-long siege of the city of Bakhmut.
Many relocated to neighbouring Belarus under the terms of the deal that ended their mutiny.
While some will be absorbed into Russia's armed forces, a considerable portion of them are expected to be angry over the sudden demise of Mr Prigozhin, who commanded a good deal of loyalty from his men.
There are also reports of makeshift memorials to Prigozhin springing up across several Russian cities.