Portsmouth have been deducted 10 points after exiting administration.
The south coast club, who had been in administration for more than a year, were this week taken over by the Pompey Supporters' Trust.
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, the penalty hardly makes any difference, whereas there had been speculation the deduction would be carried over to next season in npower League Two.
Instead, they have slipped from 22nd to the bottom of League One.
The 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."
Football League chairman Greg Clarke said: "I would like to welcome the Pompey Supporters' Trust to the Football League and pay tribute to their efforts to save their club. They have galvanised the club's fans and the city of Portsmouth behind their cause and ensured that it continues to have a professional football club.
"However, the hard work is only just beginning and we will continue working with the new owners to help them establish a sustainable future for Portsmouth Football Club, so that it can put its long running financial troubles behind it for good."
New Portsmouth chairman Iain McInnes told the club website: "We are grateful to the League for confirming this punishment will be activated in the current season."