The midfielder had previously joined the Latics on loan for the 2014-15 campaign but now signs a four-year deal with the Championship outfit, to Uwe Rosler's delight
The Wales international originally agreed a loan deal until January with the Latics as he signed a two-year deal with City but, following James McArthur's move to Crystal Palace, Uwe Rosler has moved to make the signing permanent.
The 20-year-old has put pen to paper on a four-year deal with the Championship side and Rosler is thrilled to have completed the deal.
"Emyr has impressed everyone since arriving at the club and we feel that he can have a major role to play in the future of the club," he told the club's official website.
"Everybody can see what a very talented player Emyr is and, from the first training session with us leading through to the games he has played, he has been very good.
"At just 20-years-old he is already with the full Welsh national team and the chance to sign him on a long-term contract was too good an opportunity to turn down."
Huws becomes the third player to depart the Etihad Stadium on transfer deadline day following loan moves for Micah Richards and Alvaro Negredo to Fiorentina and Valencia, respectively.