Wycombe were initially fined £10,000 by the Football Association for breaching agent regulations, which are believed to be in relation to winger Matt Phillips' sale to Blackpool in 2010.
Rovers then fell out of the Football League on goal difference after a defeat to Mansfield Town helped keep Wycombe safe.
However, Rovers officials felt Wycombe should have been hit with a points deduction after "wrongfully obtaining a competitive advantage" courtesy of the financial benefits of Phillips' sale.
While Wycombe acknowledged wrongdoing in not disclosing the details of Phillips' ownership to the Football League, the organisation felt the club were not in the wrong.
"Having fully investigated the matter, it is our view that the financial transaction in question did not amount to third party investment or influence over players," said a Football League spokesperson.
"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.
"Having co-operated fully with the investigation throughout, Wycombe Wanderers have admitted this breach of League regulations. The club has been issued with a reprimand that will remain on file for two years, as well as a warning as to its future conduct."
