(CNN) -- Arsenal's passage through to the knockout stages of the Champions League took a severe knock on Tuesday night as they went down to a shock 0-2 defeat at Braga in Group H.
Two late goals from Brazilian striker Matheus mean Arsenal relinquish their place at the top of the table and means Arsene Wenger's team with need to get a result against Partizan Belgrade in their final match.
Arsenal will complain that they had a cast iron penalty denied by the officials, when Carlos Vela was brought down in the box in the 80th minute.
But the referee didn't see it that way and booked the Mexican striker for diving.
Moments later, Matheus evaded Arsenal's offside trap before executing a cool finish over a flailing Fabianski in goal.
The Gunners misery was compounded when Matheus broke through again in injury time, weaving through a series of tackles, before firing precisely into the top corner.
In the other Group H game Shakhtar Donetsk earned a comfortable 3-0 win over strugglers Partizan Belgrade with second half goals from Stepanenko, Jadson and Eduardo.
MSK Zilina threatened to add to Chelsea's recent Premier League woes when they took a shock first half lead at Stamford Bridge in Group F.
Babatounde finished off a flowing movement to fire past keeper Ross Turnbull after 19 minutes.
They maintained their lead until six minutes into the second half when Daniel Sturridge equalized for the Blues.
Florent Malouda sparred any blushes when he scored four minutes from time to maintain Chelsea's 100 percent record in Europe this season.
In the group's other game, Marseille inflicted a 3-0 defeat on Spartak Moscow at the Luzhniki Stadium, Moscow.
Nicolas Valbuena opened the scoring for the visitors with a pinpoint strike after 18 minutes, while Loic Remy added a second shortly after the break, dinking the ball over a defender before firing home -- the ball rebounding off both posts before finding the net.
A red card for Brazilian striker Welliton in the 65th minute made a Spartak comeback even less likely.
And so it proved as Brandao added a third three minutes after Welliton departed.
The win moves Marseille up into second place in the group on nine points, which is enough for them to qualify for next year's knockout phase.
First half goals from Benzema and Arbeloa were followed by a brace from Cristiano Ronaldo in the second as Real Madrid coasted to an easy 4-0 win over Ajax at the Amsterdam Arena.
But Madrid's evening was soured when first Xabi Alonso then Sergio Ramos were sent off for time-wasting late in the game.
The win means they maintain their unassailable lead over AC Milan at the top of Group G.
The Serie A leaders left it late to secure their place in the knockout stages.
Zlatan Ibrahimovic scored his fourth goal in five Champions League games in the 65th minute, followed by an injury time strike from Ronaldinho to beat bottom placed Auxerre 0-2.
Roma completed a memorable second half comeback against Bayern Munich in the Stadio Olimpico in Group E.
Two goals from Mario Gomez in the 33rd and 39th minutes gave Bayern, who had already qualified before tonight's match, a first-half lead.
Roma halved the deficit four minutes into the second half thanks to a goal from striker Marco Borriello, but Roma fans were kept waiting until the 81st minute for the equalizer from De Rossi.
Second half substitute Francesco Totti completed the turnaround when he converted an 84th minute penalty to put Roma within touching distance of the knockout phase.
In the other Group E game, a 15th minute strike from Federico Almerares was enough to give Basle a 1-0 win over CFR Cluj-Napoca.