Bayern Munich dropped their first points of the group stage as Napoli battled back to earn a draw in Italy after Toni Kroos' opener.
Holger Badstuber's own goal ended Manuel Neuer's streak of 1147 minutes without conceding a goal, but Mario Gomez should have stolen all three points, but his spot kick was comfortably saved by Morgan De Sanctis.
The pair now have Manchester City for company after their late win over Villarreal, who now look dead and buried in the group.
Cani netted the Spaniard's first goal in the group after just four minutes, but Carlos Marchena's own goal and Sergio Aguero stoppage time winner keeps Roberto Mancini's men in the hunt
One of the more open groups at this stage, saw CSKA Moscow and Inter Milan gain a foothold on matchday three.
CSKA striker Seydou Doumbia's double sandwiched Aleksandrs Cauna's second half goal to help overcome Trebzonspor, while in France, Giampaolo Pazzini's first half volley secured Inter all three points against Lille, leaving them bottom of the group, and on the brink of elimination.
Last year's runners up Manchester United needed two Wayne Rooney penalties to beat Otelul Galati, with Milan Perendija and Nemanja Vidic sent off for both sides in a scrappy affair.
Benfica require a win in the return game with Basel to ensure progression to the last 16 after a stylish performance saw them beat the Swiss side.
Bruno Cesar finished off a a flowing first-half move, before Oscar Cardozo's free-kick confirmed the win.
Real Madrid are on the brink of qualification after they strolled past Lyon to continue the only 100 percent record in the competition.
Karim Benzema set the ball rolling, before Sami Khedira netted his first Madrid goal.
Hugo Lloris then turned in Mesut Ozil's shot before Sergio Ramos half-volleyed a fourth.
Ajax are now favourites to claim that second qualification spot, following a comfortable win over whipping boys Dinamo Zagreb with Derek Boerrigter and Christian Eriksen rounding off a comfortable win.
Bayern Leverkusen and Chelsea put themselves within a win of qualifying for the knock-out phase after important wins on matchday three.
Jonas' early goal was cancelled out by two quick-fire goal from Andre Schurrie and Sidney Sam to put the German's in pole position.
Chelsea meanwhile, thrashed Belgian side Genk at Stamford Bridge, with Raul Meireles, Fernando Torres' double, Branislav Ivanovic and Salomon Kalou piling on the misery.
Aaron Ramsey sent Arsenal top of the group with a stoppage time winner over Marseille, leaving them needing a win in the return fixture to qualify for the second round.
The fight for second is hotting up however, as Olympiakos won their first game of the group stage over German champions Borussia Dortmund.
Robert Lewandowski had cancelled out Jose Holebas' early opener, but Rafik Djebbour and Francois Modesto assured the Greek side of the three points.
Little was decided in the tightest group of all on matchday three, with all four sides in with a genuine chance of qualifying.
Shakhtar Donetsk and Zenit St Petersburg shared an entertaining draw, with Willian's first half stunner being cancelled out by Roman Shirokov before Luiz Adriano's close range finish was equalled by Victor Fayzulin with a cheeky lob.
Porto came unstuck in their attempts to beat APOEL, who stay top of Group G as Ailton's goal matched Hulk's free-kick.
AC Milan and Barcelona continue to dominate their Champions League group after comfortable wins on Wednesday night.
Zlatan Ibrahimovic and Kevin-Prince Boateng rounded off another win for Milan at the San Siro over BATE, while Andres Iniesta and David Villa helped Barcelona overcome a plucky Viktoria Plzen.