(CNN) -- In the end, it was all too familiar.
Arsenal went out, Bayern went through -- same story, different season.
For all the talk of Arsenal being able to emulate last season's famous victory at the Allianz Arena, there was one thing sorely lacking. Goals.
That it managed to secure a 1-1 draw will provide some comfort to manager Arsene Wenger, whose club has gone nine years without winning a trophy.
A 3-1 aggregate defeat means Arsenal will now have to shift its focus to the Premier League and FA Cup while Bayern continues its quest to dominate this competition.
Last year, Arsenal arrived in Munich trailing 3-1 after a first leg where it had been taught a footballing lesson by the German giant.
On that occasion, written off by every football expert on the planet, it produced one of its finest performances of recent times to win 2-0 only to exit the competition on away goals.
A year on, Arsenal once again walked into the cauldron facing a two-goal deficit against a Bayern team 20 points clear at the top of the Bundesliga and determined to become the first club to successfully defend the Champions League title.
Wenger's side, without several injured players including Theo Walcott and Aaron Ramsey as well as the suspended Wojciech Szczesny, was always going to find the going tough.
After a rather turgid first half where neither side really managed to find its rhythm, the game exploded into life nine minutes after the interval.
Bayern broke down the right and when Arsenal failed to cut out Franck Ribery's cross, Bastian Schweinsteiger took advantage by firing home from close range.
That should have seen Bayern out of sight, but Arsenal had other ideas.
Lukas Podolski, once of Bayern, chased down Philipp Lahm and after the defender stumbled under pressure, the Arsenal forward took possession and rifled the ball past Manuel Neuer.
That signaled a period of Arsenal pressure but while the visiting side found extra space going forward, it was unable to make the breakthrough.
It was Bayern which should have won the tie in stoppage time when Arjen Robben went down in the penalty area under the challenge of Laurent Koscielny.
Thomas Muller stood up to take the spot kick but his effort was parried by Lukasz Fabianski, who then beat the Bayern forward to the loose ball.
Not that it mattered to Bayern though, which qualified for the last eight for the 13th time.
"On the day 2-0 wasn't the best result in the first leg but we still had a chance to give it our all and to get a result," Arsenal midfielder Alex Oxlade-Chamberlain told ITV.
"Bayern has weaknesses like any other team and when you score anyone can get nervous. When we did that we thought we had a chance but we just couldn't do it.
"Maybe we lacked a bit of quality with the final ball. At the top level you need that. The boys put in a great shift but we can be proud of our efforts."
Arsenal's misery was compounded by an injury to record signing Mesut Ozil, who was withdrawn at halftime with a hamstring problem.
In the night's other game, Atletico Madrid sealed its place in the quarterfinals for the first time in 17 years following a 5-1 aggregate victory over seven-time champion AC Milan.
Leading 1-0 from the first leg, Atletico, second in in La Liga, took a third minute lead through the prolific Diego Costa on its way to a 4-1 win win.
Milan equalized courtesy of former Real Madrid star Kaka but further goals from Arda Turan, Raul Garcia and Costa's second sealed the win.
"We are grateful for the support of the fans, and the truth is that the team deserves congratulating for the way it has played," Costa told Spanish television.
"We have done ourselves proud. All teams who reach the quarterfinals are very good. For now we'll just enjoy."
Manager Diego Simeone was part of the last Atletico side which reached the quarterfinals of the Champions League in 1997.
Here, he watched on as his team cruised past a troubled Milan team which has struggled so badly in Serie A this season.
Milan's defeat means there will be no Italian club in the last eight of the competition for the first time since 2009.
Costa, who made his debut for Spain last week, was the hero at the San Siro in the first leg and once again it was he who tormented Milan.
His spectacular opener set the home side on its way and even when Kaka leveled, Atletico refused to buckle.
Turan netted a classy second before Garcia headed home Koke's cross to give his side a two-goal cushion.
Costa then wrapped up the win late on with his seventh goal in five Champions League games.