Three fire trucks were called in to extinguish flames as unruly Panathinaikos fans set several sections of the stands on fire.
The start of the second half was delayed by 45 minutes as fans pelted police with flares, molotovs and missiles and was subsequently abandoned altogether with nine minutes remaining with Olympiakos 1-0 ahead through Djamel Abdoun's 51st-minute goal.
Several petrol bombs exploded close to the pitch, prompting referee Anastasio Kakos to end the match prematurely and pull the players off the field.
Twenty police officers were injured and more than 50 arrests were made, while 10 molotov cocktails, sticks, firecrackers and two knives were confiscated by the authorities, police said.
Panathinaikos captain Kostas Katsouranis said Greek soccer had been shamed.
"That was not football," Katsouranis told reporters. "Certainly it's one of the worst moments in Greek football and I don't even want to comment on the game. As a team we will just try to get on with the next matches and fight for a place in the Champions League qualifiers."
Panathinaikos' Portuguese coach Jesualdo Ferreira added: "I would have liked to talk about a great derby but unfortunately I can't because this didn't happen.
"As a professional I feel very sorry for what I saw and as a person who loves Panathinaikos, I certainly don't understand it."
Panathinaikos, who have already been punished once this season for the unruly behavior of their fans and were ordered to play a match behind closed doors, will face a disciplinary hearing on Tuesday.
League rules state that if a match is abandoned due to crowd trouble, penalties for the offending team include 0 points from that game, a fine ranging from 120,000-180,000 euros as well as point deductions.
Olympiakos are expected to be awarded a 3-0 victory, which would put them three points clear of their rivals before any point deductions.
