Unicaja Malaga, Zalgiris Kaunas and Anadolu Efes Istanbul also progressed to the second group stage, joining 11 other teams who had booked their berths with games to spare.
Bayern went through after Italians Montepaschi Siena slipped to a 64-62 home defeat by Unicaja, meaning that the German side have only pride to play for in their final match against Galatasaray on Friday.
Partizan, the 1992 winners, had to match Nanterre's result to go through and having lost to CSKA Moscow 73-62 at home despite the raucous support of passionate home fans in the Pionir Hall, they were let off the hook after the French side suffered a 95-76 home drubbing by Fenerbahce.
"Partizan have improved every week and we know they will be more competitive in the Top 16, while we needed to finish the regular season on a high note," CSKA's Italian coach Ettore Messina said.
His counterpart Dusko Vujosevic said: "Given our slim budget and injury problems, I think this is a tremendous result because the players have worked their socks off to go through.
"We also have to thank Fenerbahce and their (Serb and former Partizan) coach Zeljko Obradovic for a fully committed performance at Nanterre. In the end our fate was in their hands."
Zalgiris, who won Europe's premier club basketball competition in 1999, won the final quarter at Germany's Brose Baskets Bamberg 24-11 to scrape an 84-80 win on the back of 26 points and seven rebounds by American guard Justin Dentmon.
Efes went through despite an 86-61 home rout by Real Madrid, who finished the preliminary group stage with 10 wins from as many games along with holders Olympiacos Piraeus after the Greeks cruised to a 90-81 success at Polish outfit Stelmet Zielona Gora.
The Top 16, which starts on January 2, will feature two pools of eight teams. The top four from each pool will advance to the best-of-five quarterfinal play-offs, whose winners qualify for the May 16-18 Final Four in Milan.