Former FA Cup winners Portsmouth were hit with a 10-point penalty on Saturday after coming out of administration.
Portsmouth were officially taken over by a supporters group on Friday, allowing the troubled League One club to end a 14-month spell in administration but in the process triggering the points deduction.
The Football League had previously confirmed Pompey would be deducted the points once they came out of adminstration.
But, given Portsmouth have already been relegated from the English third tier, the penalty is actually a blessing for Guy Whittingham's team.
There had been speculation the points penalty would carry over until next season, but Portsmouth are now able to start what they hope will be a League Two promotion campaign with a clean slate.
The Football League has also put in place restrictions on the club's playing budgets and borrowing.
A League statement read: "The board of the Football League has agreed to transfer Portsmouth's share in the Football League to a consortium brought together by the Pompey Supporters' Trust, bringing an end to the club's period in administration.
"Due to the club's Company Voluntary Arrangement not being fully compliant with the Football League's insolvency policy, the board has applied the following conditions of membership - as originally outlined in July 2012.
"A deduction of 10 points to apply in the 2012/13 season (in addition to the 10 points applied for entering Administration in the 2011/12 season).
"Restrictions on playing budgets, future borrowing and loan repayments for the next five seasons."
New Portsmouth chairman Iain McInnes welcomed the decision to deduct the points now, saying: "We are grateful to the League for confirming this punishment will be activated in the current season."
Portsmouth, who beat Cardiff in the 2008 FA Cup final, have suffered a remarkable fall from grace since their Wembley triumph five years ago which was followed by the high of a 2-2 draw with Italian giants AC Milan in the Europa League just months later.
In 2010 they were beaten in the FA Cup final by Chelsea and relegated from the Premier League.
Then, in 2012, they dropped into the third tier for the first time in 30 years and this season's failure makes it three relegations in four seasons.