Wheeler played eight games in the 2019 VFL season for the Northern Blues, the VFL affiliate of Carlton.
Wheeler had committed to another season with the Blues, but his position was thrown into chaos when Carlton formally ended their alignment with the club on Thursday.
The Blues - previously known as Preston and the Northern Bullants - will end operations after 138 years of playing.
Club president Stephen Papal said while he was disappointed, the outcome was inevitable.
“To see our football club unable to continue its operations is as difficult as it gets,” Papal said.
“I can say nothing more but express my eternal gratitude to every player, coach, administrator, sponsor, member and supporter that has be part of the Northern Blues Football Club and kept us going year after year.
“Our history extends 138 years and we are proud of each and every one of those seasons. This football club has a rich history and we will do everything possible to ensure it remains in the hearts and minds of our supporters forever.”
With the Blues now vacating a spot in the VFL, it has been suggested Carlton may field a reserves side if the VFL resumes this year.
In the event it does, players previously listed with the Northern Blues - including Wheeler - will likely be in line to join the club to fill the VFL side.
“Carlton will be offered the opportunity to enter a team of our own and we would obviously be leaning heavily on existing Northern Blues players to complement our listed players,” Carlton chief executive Cain Liddle said.