The Greens, looking to finish the season on a high after falling to Olympiacos in the Greek Cup final and also crashing out of the Euroleague at the end of the Top 16, won 76-69 to seal a 3-1 win in the A1 Ethniki finals.
Olympiacos reeled off the contest’s first 11 points and trailed 19-7 with three minutes to go in the opening frame when Pana made their comeback.
Zeljko Obradovic’s men responded with a 21-4 run over the next eight minutes to lead 28-23 and they stayed in front for the remainder of the game.
The winners have now claimed every play-off title except one since 1998.
AEK Athens prevailed in the championship in 2002.
Olympiacos had captured five consecutive crowns from 1993.
Panathinaikos killed the Reds with their three-point shooting, burying eight of 19 attempts.
Big man Kostas Tsartsaris made both of his shots from long range and Drew Nicholas was two of five while Vassilis Spanoulis connected on three of his seven attempts.
Tsartsaris and Spanoulis are likely to play for Greece this summer at the FIBA World Championship.
“There is great satisfaction to win the championship,” Spanoulis said.
“We faced difficulties at the beginning because of the atmosphere but we stayed focused, we got used to the pace and we did what we had to do and got a big win and with it the title of champion.”
Panathinaikos also out-rebounded Olympiacos 36-29.
Olympiacos playmaker Milos Teodosic, the Serbia international who was voted MVP of the Euroleague this season, missed all six of his shots from long range and finished with 10 points.
He shot five of 24 (20.8%) from behind the arc in the series.
Olympiacos trailed by nine points but staged a late rally and closed the gap to 73-69 on a basket by Josh Childress with 1:43 remaining.
Nicholas finished the scoring in the game with a three-point play.
The waiting game will now start for Panathinaikos and Spanoulis, one of the most famous players in Europe.
The club and the player will have contract talks but there is no guarantee he will be back for next season.
“We need to rest first and then talk about my future,” Spanoulis said.
“We’re celebrating now and will then see what happens.
“Right now I am a player of Panathinaikos.
“It’s not just in my hands.”