Having lost their first meeting in the competition earlier this year, the Greek side exacted revenge over the Germans on Friday.
Loukas Mavrokefalidis, in for the injured Esteban Batista, scored 16 points for Panathinaikos, while AJ Slaughter went one better with the biggest tally of the match.
Panathinaikos' win also confirmed Fenerbahce's spot in the Top 16, as both sides now have five wins from seven games and are guaranteed a top-four finish.
Barcelona remain top of the pool after they preserved their unblemished run with a seventh-straight win, but they needed a late score from Alex Abrines (11) to record a 84-80 victory over EA7 Olimpia Milano.
In Group A, Anadolu Efes moved level with Real Madrid at the top thanks to an 85-62 victory over Dinamo Sassari in Turkey.
Having seen group leaders Realbeaten by UNICS 24 hours earlier, Efes took full advantage as they recorded their fifth win of the season.
Dario Saric starred for Efes with 18 points and 11 rebounds, while Sassari struggled to build on an impressive second quarter that saw them score 21 points.
Also in Group A, there was a 61-55 win for Zalgiris Kaunas over Nizhny Novgorod, the Lithuanians coming back in the second half to snatch victory thanks in the main to James Andersen (18) and Lukas Lekavicius (eight).
Valencia kept their hopes of reaching the knockout stages alive in Group D with a 78-71 triumph over Galatasaray.
Kresmir Loncar (15) and Luke Harangody (13) shone for the Spaniards as they closed the gap on the other four sides chasing a qualification spot behind Olympiacos.
Meanwhile, the bottom two sides in Group B met in Zagreb, and it was the hosts who came out victorious with Cedevita beating Limoges 102-83.