The Football League has decided Wycombe Wanderers did not breach third-party ownership rules following a complaint from Bristol Rovers.
The Chairboys escaped a points deduction, but have been reprimanded for not telling the League about payments to former owner Steve Hayes.
Rovers claimed a deal by Wycombe to use sell-on clause money to pay a debt to Hayes constituted a breach of rules.
Wycombe avoided relegation on goal difference at Rovers' expense in May.
The dispute has taken more than four months to settle.
|2013-13 League Two final standings|
Wycombe's payments to Hayes became apparent during a separate legal case, in which Wycombe were found guilty of agreeing to pay an agent through a future sell-on clause in the contract of midfielder Matt Phillips.
In a statement the Football League said: "It is our view that the financial transaction in question did not amount to third party investment or influence over players.
"Instead, it was a re-organisation of Wycombe's corporate structure that saw the club reduce its debt to its previous owner.
"Nonetheless, League regulations require such agreements to be disclosed and approved by The Football League Board before they are concluded.
"It is clear that this did not happen, although it is equally clear that the Board would have approved this particular arrangement had it been given the opportunity to consider it."
After admitting a breach of League regulations, Wycombe were issued with a reprimand that will remain on file for two years.