The Saints were hoping to avoid a ten-point penalty as they argued that the club was 'unaffected by these proceedings' against the holding company.
However, a league inquiry has ruled that the ten-point penalty should apply to the Championship strugglers.
Should the 23rd-placed Saints climb out of the relegation zone in their final two games of this season then the penalty will be imposed this year and they will be relegated to League One.
But should they fail to retain their Championship status this season then the deduction will be carried over to next term and they will begin in League One next season on minus ten points.
"The board of the Football League reviewed the report of the independent forensic accountants commissioned by the League to examine the circumstances at Southampton Football Club, together with external legal advice as to the interpretation of the League's regulations," read a statement on behalf of the Football League.
"The report, by Grant Thornton, set out in detail the various inter-relationships between the four different group companies at Southampton Leisure Holdings Plc (the holding company).
"The conclusions were based both on the content of the annual accounts published by the holding company, which include the club, and other information made available to Grant Thornton as part of their enquiries."