The Owls finished 16th in the Championship, eight points clear of the drop zone.
"An independent disciplinary commission, appointed under EFL regulations, has ruled that Sheffield Wednesday will receive a 12-point deduction for breaching the league's profitability and sustainability rules for the three-season reporting period ending with season 2017-18", read an EFL statement.
The verdict was reached by an independent disciplinary commission, and has now been put to the club, though it means Wednesday will avoid relegation due to the punishment coming into play next season.
"The club is extremely disappointed that the commission has imposed a 12-point deduction to be applied next season and awaits the written reasons for this decision".
"The sporting sanction will take effect in season 2020/21".
Wednesday had denied the charge and also issued a counter-claim against the EFL for allegedly "acting unlawfully".
Sheffield Wednesday have been hit with a huge 12-point deduction after being found guilty of financial misconduct, following a lengthy investigation by the English Football League.
The EFL added that the club were not guilty of "deliberately concealing information" on the filings from the league.
The Yorkshire club were charged in November by the EFL over charges of breaching Profitability & Sustainability rules relating to the £60 million sale of their Hillsborough stadium.
"The club will await the written reasons for the sanction and upon receipt will digest and consider the full detail with its legal advisers before making any further comment".