Greece's oldest club were given until March 1st to resolve the issue and their players have since gone on strike over unpaid wages.
Having failed to improve their finances, they have been handed down a 100,000 euro fine in addition to the ban.
Panathinaikos, from Athens, are Greece's most successful side in Europe having reached the final in 1971 and the semi-finals on two occasions.
They were also given a domestic penalty of three points earlier in the year after they failed to pay money owed to former defender Jens Wemmer.
It is another sorry episode in what has been a season marked by off the field events in Greece. PAOK Salonika president Ivan Savvidis was banned after coming onto the pitch with a gun.