It ended, as it so often does these days, with the noise that is threatening to become the soundtrack to Arsenal's season. This time at least it was not as vitriolic as on other occasions and amid the boos there was even a smattering of sympathetic applause but it was scant consolation. The bottom line, ultimately, is that no team can defend this generously and expect it to lead them to ticker-tape and open-top bus parades.

Arsène Wenger will no doubt reflect with anguish on that moment, with the score 2-1 and his team threatening a comeback, when Theo Walcott crossed from the right and the substitute Olivier Giroud, barely on the pitch a minute, aimed his shot straight at Manuel Neuer. The chance was gone and it was six minutes later that Mario Mandzukic and Bacary Sagna slid in for the same low cross and the ball spun between them then dropped, almost in slow motion, over the goalline.

That was almost certainly the fatal blow that condemned Arsenal to an eighth year without a trophy. Yet the truth was Bayern will probably be aggrieved they had to wait that long. They had led 2-0 after 21 minutes, courtesy of Toni Kroos and Thomas Müller, and for long spells there was the clear evidence for why Bayern are 15 points clear at the top of their league and Arsenal 21 behind in theirs.

Wenger was right when he talked of a team that played the second half with spirit and perseverance but this was another night when their vulnerabilities were laid bare. Even when Lukas Podolski's header encouraged them to have their best period of the match the truth is the goal came almost as a shock.

Bayern had played with the command of serial champions and the sense, unlike Arsenal, that everybody fully understood his role. Those early moments, when they took control and played with the mastery and togetherness that comes from having total confidence in one another, was a stark demonstration of football played with structure and confidence.

Arsenal managed little bursts of action here and there but they have been undermined for far too long by their defending and from here it will need something close to a miracle in Munich on 13 March. The mistakes in Bayern's defence that led to Podolski's goal, most notably a rare lapse from Neuer, betrayed the fact that this team has conceded only seven goals in 22 Bundesliga fixtures and recently went almost four and a half hours without an opponent racking up a shot on target.

For Arsenal it was the same old dispiriting story. A classy strike from Kroos that gave Bayern the lead yet Wenger's shoulders will sag even more when he sees again how straightforward it was for Müller to deliver the cross. Ramsey dangled out his leg but not with any conviction.

The ball ran to Kroos, who expertly judged the bounce before demonstrating the art of striking a sideways ball first time. With great control and technique he kept his shot down and beat Wojciech Szczesny for sheer power.

Arsenal's supporters will understand a little better now why Kroos is so revered in his own country, playing at the head of a midfield bolstered by the football intelligence of Bastian Schweinsteiger and Javi Martínez. Ramsey will be able to testify for it as well, considering that moment, shortly before half-time, when Kroos cruelly slipped the ball through his legs. If ever there was an exchange that summed up the imbalance of talent, that was it: a nutmeg by the halfway line and then Bayern were breaking again.

Yet Ramsey was not the only Arsenal player to suffer in a brutal first half. The opening goal originated from Per Mertesacker needlessly giving the ball away. The same player was guilty of losing Daniel Van Buyten from the Kroos corner that led to Müller doubling the lead. It was a hideous goal to concede but perhaps the most depressing thing for Arsenal's supporters is that this is all part of a pattern.

In this parish they have grown wearily accustomed to suffering from set pieces and the sight of Mertesacker, and others, waving an apologetic hand. Van Buyten's header flashed towards Szczesny at speed but it was a poor block from an erratic goalkeeper and Müller hooked in the rebound.

Wenger's players left the pitch at half-time to sustained dissent and there was another show of mutiny when he substituted Podolski in the second half. Arsenal, however, do deserve a sliver of credit for their response after the interval, even if the goal that brought them back into the match owed a lot to Neuer's error. Bayern's goalkeeper had left his goalline to try to collect Jack Wilshere's corner but then changed his mind. Martínez, the nearest Bayern player, had become tangled with Laurent Koscielny and that left Podolski to head into the exposed goal.

Wilshere, playing with great endeavour, kept pushing his team forward but there was always the sense that they might leave themselves open again at the back. After 78 minutes the substitute Arjen Robben sent the excellent Philipp Lahm on another of his overlapping runs. The luck was with Mandzukic and, for Arsenal, the damage is surely irreparable now.