The move, announced by both clubs on Wednesday, concludes Nancy’s highly successful spell in MLS.
The clubs have been fined a combined £140,000 relating to a mass confrontation during their Championship match on 18 October.
The latest sanction comes on top of the 12-point penalty imposed on 24 October when the Owls entered administration.
The departure follows a damaging run of results that has left the club hovering near the Bundesliga’s danger zone.
The agreement follows last year’s Diarra ruling which found parts of FIFA’s Regulations on the Status and Transfer of Players incompatible with EU law.