The Belgium coach was assisted by Shaun Maloney for three years.
A three-and-a-half-year deal has been signed by the new Hibs manager.
The former Celtic and Scotland player, 38, left his role as Belgium assistant to replace Jack Ross and take on his first managerial job.
Aberdeen will be the first game in charge of by Maloney.
He will be assisted by his former team-mate Gary Caldwell, who left his post at Manchester City's academy.
After playing at Hibs, Caldwell joined Celtic and later managed Wigan, Partick Thistle and Chesterfield.
David Gray took over as interim head coach of Hibs for three games, including the Scottish League Cup final. Hibs are seventh in the league.
The goalkeeping coach and the backroom team will remain.
Ben Kensell, the chief executive of Hibs, said that this was a big opportunity for the young coach. He will be supported in the upcoming transfer windows to help achieve our goals here.
We have a lot of faith in him. He wants to bring success to the club.
After 18 months at Villa, he returned to the club and played for Wigan, Chicago and Hull. He scored seven Scotland goals.
He joined the Belgium set-up in the year after he moved into coaching with Celtic's under-20s.
An analysis 'A bit left-field'.
John Hughes was a manager.
He's a football guy, but he's a quiet kind of guy. If you don't have that personality, you need a number two that can laugh at himself, get a bit of fun, and know the game and is a good coach. The number two will be important if it is him.
The former St.
It's very in-keeping with the way that a lot of clubs are going down these days, young managers going in with different ideas, and their own philosophy on the way they want to play the game.
He has no experience in management. It's easy to talk about tactics and analyse the game, but to manage a squad of 25 people by yourself would be an eye-opener for him.
