Manchester City's first away match in the Champions League was dominated by headlines surrounding Carlos Tevez's refusal to play in the Allianz Arena, and on the pitch Mario Gomez's double before half time ensured Bayern Munich top the group, leaving Roberto Mancini's side off the pace in third.
Napoli's first half blitz against Villarreal was enough to give them their first ever Champions League victory, as Marek Hamsik and Edinson Cavani's penalty saw off the Spaniard's.
Claudio Ranieri's revolution at Inter Milan continued as CSKA Moscow were narrowly beaten at the Luzhniki Stadium.
Lucio and Giampaolo Pazzini's first half goals were cancelled out by Alan Dzagoev's stunning free kick and Vager Love's stinging shot, before Mauro Zarate's thundered the Italian's to victory.
In Turkey, Moussa Sow's narrow finish looked to have given Lille their first win of the group stage, but Gustavo Colman's 75th minute penalty keeps Trabzonspor top of the group.
Danny Welbeck's early double had sent Manchester United on their way against Basel, but Fabian Frei's half volley sparked the Swiss side's second half revival.
Alexander Frei's header and 76th minute penalty looked to have sealed a famous Old Trafford win, but Ashley Young's first Champions League goal salvaged a point for last year's runners-up.
Benfica required just one goal to overcome Otelul Galati, with Bruno Cesar poking home after Nicolas Gaitan's delicious through ball.
Two first half goals from Remi Garde's Lyon ensured they stay undefeated, as Dinamo Zagreb crashed to their second defeat of the group stage.
Bafetimbi Gomes' perfectly flighted chip opened the scoring, before the unmarked Bakari Kone doubled the advantage.
Ajax's resistance at the Bernabeu lasted just 25 minutes against Real Madrid, as Cristiano Ronaldo finished off a flowing move for their opener, before Kaka slid home to make it two and layed the ball on a plate for Karim Benzema's third.
Frank Lampard put talk of his Chelsea exit behind him with a goal just before the hour mark at the Mestalla Stadium but Salomon Kalou's handball allowed Valencia's Roberto Soldado to score the equaliser, there minutes from time.
Bayer Leverkusen are now second behind The Blues after Lars Bender stroked effort and Michael Ballack's deflected shot earned victory over plucky Genk.
Alex Oxlade-Chamberlain became the youngster ever English goalscorer in the Champions League, while Andre Santos netted his first for the club, as Arsenal stuttered past Olympiakos, who saw David Fuster give them hope with a free header.
Despite an impressive display against The Gunners on matchday one, Borussia Dortmund were overwhelmed by a free flowing Marseille at the Stade Velodrome.
Andre Ayew's drive and 69th minute penalty sandwiched Loic Remy's thunderous strike to give the hosts maximum points after two games.
The sending off of Jorge Fucile helped turn Zenit St Petersbury's fortunes around, after James Rodriguez had handed Porto the lead.
Against ten-men, the Russian's were ruthless, with Roman Shirkov first capitalising on Helton's error to level the scores, before driving a second on the hour, with Danny rounding off the victory.
APOEL produced perhaps the shock of matchday two, as they earned a valuable point against Shakhter Donetsk, thanks in part to Ivan Trickovski's neat finish, with Jadson levelling for the home side three minutes later.
A Lionel Messi-inspired Barcelona strolled past BATE Borisov in Minsk.
Aleksandr Volodko's own goal gave the Catalans the ideal start, before Pedro and then Messi's double, the second a terrific strike from the edge of the box, was capped off by David Villa's late goal.
AC Milan keep pace with Barca as they overcame Viktoria Plzen with Zlatan Ibrahimovic's penalty and Antonio Cassano's fine finish capping an impressive display for the Serie A strugglers.