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.
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.
Geelong chief executive Steve Hocking previously defended the deal, saying there was "not a lot" the club would change in how it had dealt with the issue.
The Cats had reached a deal with Kolodjashnij in 2024, requiring him 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.
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