Elsewhere, Istanbul rivals Galatasaray sealed a Top 16 berth with a 78-70 home win over Unicaja Malaga.
Panathinaikos, who have also lifted Europe's premier club trophy six times, joined Galatasaray in the second group stage with a 69-63 defeat of Red Star Belgrade and Basque outfit Laboral Kutxa Vitoria advanced after a 79-63 victory over Lietuvos Rytas Vilnius.
Having lost to Fenerbahce by 26 points in the reverse fixture, CSKA came out looking for revenge but were undone by superior long-range artillery as the visitors nailed 12 three-pointers while the Russian giants managed only half as many.
"We are where we should have been one month ago but if we keep working hard hopefully we will hit top form some time soon," CSKA coach Ettore Messina told www.euroleague.net after seeing his team suffer a third defeat.
Messina's counterpart Zeljko Obradovic said: "This is still the beginning of the tournament. The Top 16 is ahead and anything can happen. I asked my players to forget the first encounter with CSKA and they showed character."
Panathinaikos came out on top in their dogfight against Red Star thanks to a blistering first-half performance from guard Ramel Curry who finished with a personal Euroleague high of 16 points while forward James Gist added 15.
Laboral Kutxa cruised to their third successive win on the back of 17 points by Lamont Hamilton and 12 from Fernando San Emeterio while former NBA journeyman Carlos Arroyo carried Galatasaray with 22 points and five assists.
Holders Olympiakos Piraeus and last season's finalists Real Madrid extended their perfect starts to eight wins.
Both teams had already booked their passage alongside Barcelona, Fenerbahce, CSKA, Maccabi Tel Aviv and Russians Lokomotiv Kuban.
Olympiakos edged out newcomers Bayern Munich 105-103 in a free-scoring encounter, forward Stratos Perperoglu scoring 25 points and inspirational playmaker Vassilis Spanoulis chipping in with 24.
"I am a fan of the Olympiakos style because they have played excellent basketball for a long time and tonight I think everyone can be happy," said Bayern's Serb coach Svetislav Pesic who guided the former Yugoslavia to the 2001 European Championship and the 2002 world title.
"We didn't win the game but we won the second half by seven points and that's the reason we can be proud...we still have hopes of reaching the Top 16."
Real survived a late onslaught to beat Emporio Armani Milan 78-71.
The second group stage features two pools of eight teams. The top four from each advance to the best-of-five quarter-final playoffs.
The Final Four is in Milan from May 16-18.