Euroleague Basketball, the premier club competition's ruling body, punished the Greek side for the use of illegal sirens, flares and firecrackers as well as for breaching the official capacity of their OAKA Arena for the two matches against Barca.
"All visiting teams must assume that, whenever they come to Athens, they are very likely to face unsportsmanlike conduct from some home spectators as well as disturbance of all sorts and nature," the league said on the competition's official website.
"Euroleague Basketball's independent disciplinary judge made specific emphasis to the list of violations recurring at Panathinaikos home games during the last two seasons and on the potential physical danger to fans, players and game officials due to the ongoing violations."
Earlier this month, Panathinaikos were fined £125,000 after their president Dimitris Giannakopoulos accused officials of showing bias in a 72-70 defeat by Barcelona in the first game of the series.
Barcelona, who then fell behind after losing the next two games, won 3-2 after levelling the series with an emphatic win in Athens and clinching the tiebreaker 63-54 on their home court to reach the May 10-12 Final Four in London's O2 Arena.
Six-times Euroleague champions Panathinaikos were also fined £7,500 for trouble their fans caused during a regular-season home game against CSKA Moscow on April 4.
Barcelona will meet eight-times winners Real Madrid while holders Olympiakos Piraeus take on CSKA in the semi-finals on May 10. The final and the third-place match will be played two days later.