The versatile 21-year-old, who had two loan spells with the Owls last season, has put pen to paper on a four-year contract.
"We are delighted to get the boy back because we have done a lot of hard work to get him here," manager Dave Jones told the club's official website.
"Other clubs were aware of what he did here last season and wanted him on board, but he really enjoyed his time here and wanted to come back.
"To get Jeremy on a permanent transfer represents a really good signing for the football club and is a statement of intent because he is a really talented footballer, he is young and has a terrific future in the game."
Helan, a product of City's academy who has also had loan spells at Carlisle and Shrewsbury, made 28 appearances for Wednesday last season and was comfortable at both left-back and wide midfield.
He initially arrived at Hillsborough in November and his loan deal was extended in January until the end of the campaign.
- Sports & Recreation