"Since this issue arose we have been working hard behind the scenes to find a resolution and to help the player obtain the relevant documentation," Chief Executive Mark Ashton told the clubs official website.
"However, this has not been possible and today we have released Junior from his contract.
"Having conducted ourselves entirely correctly with the football authorities as we sought to complete the registration process it is extremely frustrating to lose a player in this fashion."
The 29-year-old Brazilian forward had penned a two-year deal at Vicarage Road back in July but that contract has now been cancelled.