The Board of The Football League confirmed the sanction after a consortium led by the Pompey Supporters' Trust successfully brought the struggling club out of administration
The club had been in administration since February 17 2012 and came close to being liquidated before the the Pompey Supporters' Trust successfully completed a takeover.
Pompey feared the points deduction would be carried over into next season but to their relief the Football League announced the punishment would come into effect straight away.
Iain McInnes, chairman of Portsmouth Community Football Club, said in a statement: "We are grateful to the League for confirming this punishment will be activated in the current season."
An out-of-court settlement between the former owners and administrators allowed the hand over of the south-coast club who have already been relegated from League One.
"I would like to welcome the Pompey Supporters' Trust to the Football League and pay tribute to their efforts to save their club," said Football League chairman Greg Clarke told reporters.
"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.
"This has been an extremely challenging situation for the Football League, given the level of debt, the length of the administration and the issues surrounding the ownership of Fratton Park. I take my hat off to everyone involved, as it has taken significant amounts of hard work, clear thinking and resolve to achieve this outcome.
"Finally, I would like to pay tribute to Portsmouth supporters for giving their financial backing to the Trust's rescue plan and for turning out in force throughout the administration as it has kept the club in business. Hopefully, this marks the start of a better future."
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