A Michael Owen hat-trick saw Manchester United claim top spot in Group B with a 3-1 win at Wolfsburg. Meanwhile, Bayern Munich stormed into the last 16 with a 4-1 win at Juventus and AC Milan and Real Madrid both qualified for the knockout stages.
Needing a point to secure top spot, an unfamiliar United defence that included Darren Fletcher and Michael Carrick looked unconvincing as Wolfsburg wasted a number of clear chances in the first half in Germany, but Michael Owen gave the visitors an undeserved lead when heading home just a minute before the break.
In the knowledge that CSKA were leading Besiktas at half-time and therefore sneaking into second place, Wolfsburg emerged with purpose for the second half and reputed United target Edin Dzeko headed his side level on 56 minutes. But Michael Owen secured top spot for United when tucking home his second after good work from Gabriel Obertan after 83 minutes and completed his hat-trick when rounding off a quick break with a masterful dinked finish.
Defeat meant that Wolfsburg were left to contemplate a place in the Europa League as CSKA, dealing with the fall-out from a drugs controversy, defeated Besiktas 2-1 in Turkey. Milos Krasic struck first for CSKA and although Bobo equalised, Evgeni Aldonin netted deep into injury time to send the Russians through to the knockout stages for the first time.
However, CSKA's place in the competition remains at risk after Alexei Berezutsky and Sergei Ignashevich tested positive for a banned stimulant. UEFA will hear the case on December 17 and under the governing body's rules, the Russia side could be expelled from the competition.
Group A came to a thrilling conclusion as Bayern Munich answered their critics with a thrilling 4-1 victory at Juventus, handing them a place in the knockout stages at the expense of the Italian club, who needed only a draw to take second place behind Bordeaux.
David Trezeguet made a bit of history for Juventus when his expert finish after 19 minutes gave the Italian side the lead. It was Trezeguet's 168th goal for the Bianconeri, making him the club's highest ever foreign goalscorer, surpassing Omar Sivori.
Bayern responded in unusual circumstances when goalkeeper Hans-Jorg Butt scored from the penalty spot on the half-hour mark and Louis van Gaal's side took the lead in the second half when Ivica Olic pounced after Gianluigi Buffon turned Daniel van Buyten's header into his path. Goals from Mario Gomez and Anatoliy Tymoshchuk sealed a famous win which means Juventus go into the Europa League.
Bordeaux had already won the group and a Jussie goal after 13 minutes ensured they finished with 16 points from their six games with a win at Maccabi Haifa. The Israeli side finished without so much as a point or a goal and are the first team to set that unwanted record.
In Group C, Real Madrid claimed top spot with a 3-1 win over Marseille while a 1-1 draw at FC Zurich was enough for Milan to claim the second qualification spot. Cristiano Ronaldo, sent off at the weekend, put Real in front with a stunning free-kick after only five minutes for his fifth goal in four Champions League games for Real Madrid, but Marseille responded six minutes later when Argentinian Lucho Gonzalez struck at Stade Velodrome.
Raul Albiol claimed his first goal for Real on the hour mark after Marseille failed to clear a corner and the home side had the chance to respond again when Iker Casillas felled Mamadou Niang in the box. Lucho smacked his penalty against the crossbar though and Ronaldo claimed his second with ten minutes remaining.
Milan made hard work of beating Marseille into second as they were forced to come from a goal down to defeat FC Zurich. Having already lost to the Swiss side at home, Milan found themselves a goal down when Milan Gajic struck after 29 minutes. A red card shown to Alain Rochat allowed Ronaldinho to equalise from the penalty spot in the second half.
Chelsea had already topped Group D but suffered a disappointing evening when drawing 2-2 with Apoel Nicosia. In an eventful first half at Stamford Bridge, Apoel took a shock lead through Marcin Zewlakow but Michael Essien hit back with a long-range effort before being forced off with a suspected hamstring strain. As Chelsea reshuffled following the loss of the midfielder, Didier Drogba scored his third goal in three Champions League games this season when finishing off a nice move but Nenad Mirosavljevic equalised with three minutes remaining.
Meanwhile Porto, already guaranteed of second place, turned on the class against Atletico Madrid when goals from Bruno Alves, Falcao and Hulk saw the Portuguese side secure a 3-0 win at the Vicente Calderon. Atleti still took the Europa League spot due to Apoel's draw against Chelsea.