Roma rallied from two goals down to beat last season's runners-up Bayern Munich 3-2 and take a big step toward advancing from the group.
Bayern, who had already qualified and will go through as group winners, went into a 2-0 lead through two quick goals from Mario Gomez.
But the Italian outfit made a remarkable second-half comeback with goals from Marco Borriello, Daniele de Rossi and a penalty from substitute Francesco Totti earning them the win.
The result puts Roma within touching distance of the next round as they sit three points clear of third-placed Basel, who beat Cluj 1-0 courtesy of a Frederico Almerares goal after 14 minutes.
Marseille cruised into the last 16 with a 3-0 victory over Spartak Moscow at the Luzhniki Stadium.
Mathieu Valbuena got Didier Deschamps' men off to the perfect start with a fine opener inside 20 minutes, and further strikes by Loic Remy and Brandao after the break ensured Marseille earned the margin of victory they required to progress.
But the Blues had to come from behind to pick up the three points against the European minnows after Babatounde Bello gave the visitors a shock 19th-minute lead.
Goals from Daniel Sturridge and Florent Malouda meant Chelsea maintained their perfect record in the competition.
AC Milan sealed their spot in the last 16 after a less than convincing 2-0 victory over Auxerre in Burgundy.
Zlatan Ibrahimovic's wonderful 64th-minute strike came out of the blue and put them in front, while Ronaldinho came off the bench to curl in a second late on.
The win leaves Milan on eight points in Group G, and Ajax's 4-0 thumping at home to Real Madrid ensured the Rossoneri will qualify as runners-up to the Spaniards.
Cristiano Ronaldo took his tally to 19 goals in 19 games as Madrid guaranteed themselves first place in the group after convincingly seeing off the hosts at the Amsterdam ArenA.
Goals from Karim Benzema and Alvaro Arbeloa put Madrid in control with Ronaldo scoring twice after the break, the second a penalty.
But Madrid finished the match with nine men after Xabi Alonso and Sergio Ramos picked up second yellow cards from Scottish referee Craig Thomson for blatant time-wasting, meaning both players will serve their one-match suspension in the last group game.
Ramos insisted Madrid had not hatched a plan and manager Jose Mourinho, when asked about the red cards, said: "I spoke with many players throughout the game, not only with Ramos and Alonso.
"Stories sell, but the important thing is the 4-0 win and the fantastic game we had. Let's talk about that and not other things."
Shakhtar Donetsk scored three second-half goals to brush aside Partizan Belgrade and virtually assure their progress.
Goals from Taras Stepanenko, Rodrigues Jadson and ex-Arsenal striker Eduardo helped Shakhtar collect the three points and add to pointless Partizan's European misery.
The Gunners were denied what looked like a certain penalty by referee Viktor Kassai before Braga scored two late breakaway goals from Brazil striker Matheus, leaving Arsene Wenger's men waiting to secure a place in the last 16 as they are level on points with Braga.
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