The match was later abandoned after a group of home Olympiakos fans refused to leave the arena.
Having taken a 2-0 lead in the best-of-five series, Panathinaikos were leading the match 76-72 with 1 minute 27 seconds to play when fans invaded the court and showered Panathinaikos players and officials with missiles and flares.
A league spokesman confirmed the match had been awarded to Panathinaikos and they were now champions for the 33rd time.
Greek sport has been plagued with fan violence during the country's economic woes.
Olympiakos can expect a heavy punishment from the Greek authorities, having received a six-match supporter ban for a similar offence in the playoff finals two years ago when Panathinaikos again clinched the title in Piraeus.
- Sports & Recreation