All 16 top flight clubs had their licences reviewed by the Hellenic Football Federation (EPO) licensing committee, and while eight teams were approved, the other eight - including Panathinaikos - had their initial submissions rejected seven days ago.
However, following an appeal hearing that lasted until the early hours of Friday, Panathinaikos, PAS Giannina and Panthrakikos, secured top flight football for the 2013-14 season.
"The appeal body of the Hellenic Football Federations Licensing Committee ... has accepted and grants permission for all three clubs to participate competitively in the 2013-2014 season," the national body said in a media statement.
OFI Crete, Aris Salonica and Panionios still have appeals pending.
The eight clubs initially awarded licences were Olympiakos, PAOK Salonica, Asteras Tripolis, Veria, Skoda Xanthi, Atromitos Athinon, Levadiakos and Platanias.
The decision comes as a huge relief in particular to PAS Giannina, who have qualified for Europe for the first time, and Panathinaikos, who endured a terrible season.
Panathinaikos went through four coaches last season and failed to qualify for Europe for the first time since 1997.
Last season was supposed to herald the start of an optimistic new chapter under fan ownership after the transfer of the Vardinoyiannis family's majority shareholding to the new 'Panathinaikos Alliance' was completed last year
But under president Giannis Alafouzos the club have struggled financially and were forced to part with Greece internationals such as Kostas Katsouranis, Loukas Vintra, Nikos Spiropoulos and Lazaros Christodoulopoulos during the season.
Arch-rivals Olympiakos Piraeus also won their 40th league title while Panathinaikos finished ins sixth place, 37 points behind their Athens neighbours.
- Sports & Recreation
- PAS Giannina