The Gunners lost 5-1 at the Emirates Stadium, with their thrashing by the same scoreline in the first leg in Germany condemning them to an embarrassing 10-2 aggregate defeat.
James Olley assesses the key talking points for the Gunners...
Arsenal’s Champions League curse strikes again
The Gunners were unlucky to draw Bayern Munich having topped the group but the bottom line is Arsene Wenger’s side have been knocked out at the last 16 stage for the seventh consecutive season.
Once again, the contest was lost in the first leg as Arsenal capitulated in the Allianz Arena by conceding three goals in 14 minutes after Laurent Koscielny limped off with an injury; they paid dearly for an immaturity in appreciating the tie was 180 minutes long.
More than that, Arsenal were simply not good enough to compete at the highest level and after more than £85million investment in a squad Wenger had huge faith in, it is a damning indictment of the manager and this group of players.
Wenger’s future must be decided soon
The Frenchman is adamant he wants to wait until the end of the season before deciding whether he will step down as Arsenal manager but this was a hugely embarrassing result which only adds to the sense the club is stagnating in the uncertainty.
A 10-2 aggregate defeat in the competition he wants to win more than any other will rank as one of the most painful experiences of his entire career and it is difficult to imagine the results required from here until May to convince the majority Wenger is the right man to continue at the helm.
The board will back him in spite of this, however, but perhaps not even a second place finish and an FA Cup win would be enough to create the feeling they are still moving forward. There are hugely testing times ahead.
Fans protest inside and outside Emirates Stadium
Only around 200 supporters joined a march outside the ground prior to kick-off in opposition to the board’s decision to offer Wenger a new two-year contract and so perhaps of greater significance were the empty seats inside the ground.
Many season-ticket holders were looking to resell their seats through the club’s exchange facility but it did not prevent a plethora of spaces, particularly around the upper tier.
An accurate figure is always difficult to gauge given Arsenal frame their attendances in terms of tickets sold – 59,911 in this case - but approximately 3-5,000 seats were not taken; the tie was virtually a lost cause but this was still Champions League knockout football.
Those inside the ground backed Arsenal in a spirited display but the apathy from those who did not turn up was another blow to Wenger’s hopes of keeping the majority onside.
A section turned their ire to majority shareholder Stan Kroenke in the second half, urging him to “get out of our club”. Bayern supporters, for their part, also protested – not for the first time here - against the £64 cost of an away ticket.
Spreading illness a cause for concern
Alex Iwobi was taken ill on the day of the game but Arsenal’s pre-match problems did not end there.
Danny Welbeck also suffered an illness in the warm-up – using Twitter to declare: “no injury, no tweak, just ill at the wrong moment” – prompting a late reshuffle.
Iwobi’s absence had forced Ozil to take a place on the substitutes’ bench a day after Wenger stated he was “not physically ready to be in the squad”.
An Arsenal spokesman insisted the illnesses were not related but to have three players suffering from three separate bouts of sickness at the same time seems somewhat unusual.
Theo Walcott makes his point
Walcott was left on the bench for Arsenal’s last two high-profile matches – the first leg against Bayern and Saturday’s defeat at Liverpool – so he had something of a point to prove here.
The 27-year-old was at the heart of everything positive for the home side in the first half, playing with pace and purpose before thrashing a 20th minute shot past Bayern goalkeeper Manuel Neuer from a tight angle.
Walcott has now scored four goals in as many home Champions League matches and although his efforts were in vain as Bayern ran riot after the interval, he advanced his case for greater involvement in the challenges ahead.