But Fifa and Uefa refused to recognise the new structure as they do not accept political interference in national associations, and the Polish National Olympic Committee must now withdraw the temporary administrator.
The Polish government has agreed to end its administration of the PZPN and adhere to a "roadmap" set up following a similar row in 2007.
Failure to comply would have meant Poland faced being handed automatic 3-0 defeats in their upcoming World Cup qualifiers against the Czech Republic and Slovakia, but those matches will now take place.
Uefa had also threatened to take Euro 2012 away from Poland - co-hosts along with Ukraine - if it failed to reinstate its Football Association.
That remains a possibility as Fifa says it will continue to "closely monitor the situation at the Polish FA and the implementation of the measures established in the roadmap".
The roadmap was created following discussions between the Polish FA, the Polish government, Fifa and Uefa and laid out the steps that should be taken before elections take place at the Polish FA.
The matter will be analysed and discussed at the next Fifa Executive Committee meeting on 23-24 October.
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