The High Court had been due to analyse issues - relating to the sale of Portsmouth's Fratton Park stadium - which hindered the takeover by the Pompey Supporters' Trust (PST).
But lawyers representing administrators and the former owner told a judge in London that an agreement had been reached.
Portsmouth was placed into administration in February 2012.
Pompey have become the biggest fan-owned club in the country after it was announced in the High Court that the club's administrators BDO had agreed a settlement deal with Portpin, a holding company run by former club owner Balram Chainrai, Levi Kushnir and Deepak Chainrai, who controlled Fratton Park.
Portpin had placed a value of £10million on the club's stadium, while the PST had bid £3million and without a compromise agreement the fans' attempts to complete a takeover would have been dashed.
PST chairman Ashley Brown welcomed the agreement, saying in a statement: "This is a historic day for Portsmouth Football Club and for Pompey fans everywhere.
"At last, the tough work done over the last year is over and we can start to rebuild our club. Pompey fans are now days away from owning and running our club and becoming the biggest community owned football club in the country.
"We have a lot of people to thank, and much more to say, but will do that once the details of the settlement are finalised. For now, we would like to offer heartfelt thanks to Pompey fans all over the world who have pledged money and have saved our club from liquidation.
"Now the next chapter of hard work begins to transform our club into something the community of Portsmouth can be proud of, both on and off the field."