An out-of-court settlement between the former owners and administrators for ownership of Fratton Park meant the takeover was completed on Friday.
The 2008 FA Cup winners, who saw their relegation to League Two confirmed on Tuesday, have been close to liquidation over the past 14 months, having been in administration since February 2012.
While potential buyers included former owner Sulaiman Al Fahim, as well as former Watford owner Laurence Bassini, the bid from the supporter-led consortium - backed by wealthy investors - was maintained.
A total of nearly £3m was raised, with fans pledging £1,000 to be part of the Trust, which was added to by a £1.45m bridging loan, as well as investment from their property partner Stuart Robinson.
Trevor Birch, joint administrator of Portsmouth, said: "We have cleared the final hurdle: all of the paperwork has now been signed and the sale concluded.
"It has taken more than 14 months of hard work from all concerned to get here and there were many times over that period when I didn't think we would make it; but we have, and Portsmouth Football Club can once again look forward to the future with optimism.
"The PST has shown what can be achieved when fans unite together for the good of their community. The club has been through considerable turmoil over the last few years, and I hope it can now enjoy a period of stability and the chance to build solid foundations for a sustainable future based on hard work and honest endeavour."
Ashley Brown, Chairman of the Pompey Supporters' Trust, said: "What a momentous day! Once again Pompey fans have shown why they are some of the best in the land, we now have a club owned by people who truly love it, its fans. That's how football is supposed to be."
Iain McInnes, Chairman of Portsmouth Community Football Club, said: "It has been a very difficult journey to get to this point but in the end we have achieved the right result.
"Now is the time for Pompey fans to get behind the club and we are looking forward to celebrating becoming a community club at Fratton Park this Saturday afternoon."