The penalty is $100,000 plus a suspended sanction of $40,000, which stems from the league fining Geelong in October after an investigation into the club's third-party agreements.
James Peters KC was brought in by the AFL to investigate Geelong, after the league had issued a "please explain" when the revelation about Kolodjashnij's contract broke this month.
Peters found the failure by Geelong to lodge the variation was an oversight, and that the club did not intend to conceal the existence of the agreement or deceive the AFL or the AFL Players Association.
Kolodjashnij, the 2022 Cats premiership defender who has not played since the story broke, returned to training this week ahead of the finals
Peters investigated the inclusion of a waiver in Kolodjashnij's 2024 contract, which followed several concussions.
The review found Geelong had given careful and detailed consideration to the risk of Kolodjashnij continuing to play, after an uncertain outcome from his assessment by the AFL concussion panel.
It found Geelong consulted extensively with the AFL, club doctors, lawyers and insurers, as well as Kolodjashnij and his family.
But the agreed waiver was not provided to the AFL or AFLPA and it was not lodged as required under AFL Rules.
The AFL Commission accepted the findings of the review.
"The review found Geelong breached AFL Rules by entering into an unauthorised variation to a player's contract and failing to lodge that document with the AFL and AFLPA," commissioner Paul Bassat said in a statement.
"The health and safety of our players is our highest priority and the Commission is satisfied it was central to the decisions made by the Geelong Football Club.Â
"While the review found no intention to conceal the document or deceive the AFL or AFLPA, the Commission determined the rules were breached and that a significant sanction was warranted."
Bassat added that clubs are expected to comply with the rules and processes designed to protect players and the integrity of the game.
"It is clear this incident goes beyond the breach of lodgement rules, and has raised broader issues to do with informed consent in playing contact sport and the paramount responsibilities for players' health and safety," Bassat said.
"Working with the AFLPA, medical experts, and other stakeholders, the AFL will have more to say on these significant policy matters."
Geelong chief executive Steve Hocking previously defended the deal with Kolodjashnij, saying there was "not a lot" the club would change in how it had dealt with the issue.
The parties had reached a deal in 2024, requiring Kolodjashnij to take all legal responsibility for future brain trauma, so he could keep playing at the club.
On the weekend, current Geelong president Grant McCabe referred to it as a "voluntary assumption of risk" and said there was extensive consultation when the agreement was reached - including with AFL officials.
The revelation had put pressure on Hocking and current AFL chairman Craig Drummond, who was Geelong president when the waiver was signed.
Hocking and Drummond avoided individual sanctions, with Peters' review finding there was no "inappropriate or improper conduct warranting additional action" by Geelong or AFL representatives.
Geelong's $140,000 fine will be paid into the AFL and AFL Players Association players' injury and support fund.
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