Without Manuel Neuer, Arturo Vidal and Kingsley Coman for both the first leg at home and the second last night in the Santiago Bernabeu, Jupp Heynckes then had to deal with injuries which kept David Alaba out of the first game and Arjen Robben, Jerome Boateng and Javi Martinez out of the second.

Those losses were overwhelming and it will forever remain unknown what Bayern could have done if they had their full complement available.

To compound matters it was Rafinha – replacing Alaba in the Allianz Arena last week – who made the mistake to permit Marco Asensio to score the crucial second away goal which ultimately dragged Bayern under. It was Sven Ulreich – a capable deputy to Neuer in the Bundesliga all season long – whose FIFA glitch moment gave Karim Benzema his second goal at the Bernabeu.

He was dealing with a back-pass that could have been played better by Corentin Tolisso, who might not have played had Vidal or Martinez been fit to start.

“We were overall superior but have given Real a goal in both games and that is blatant at this level,” defender Mats Hummels told Sky on Tuesday night. 

It was again one of those moments where Real Madrid emerge victorious and you’re left asking just how they managed it. They are heading to a fourth Champions League final in five seasons and still people are left with doubts over whether they are indeed the best team in Europe.

They seem to lack a rhythm, a fluency and a game plan. Their mode of operation against Bayern over two legs appeared to be survival.

Raphael Varane and Sergio Ramos threw themselves in front of any goal-bound shot at the Bernabeu and the ones that they missed were mopped up by a much-criticised goalkeeper who stood up under scrutiny in Keylor Navas.

But survive they did. Bayern are left bemused and bitterly disappointed.

“We played a superb game today and were the better team over both matches,” said Heynckes to Sky . “But Real Madrid is Real Madrid. Normally two goals in the Bernabeu are enough for a win. We deserved to be in the final.”

It’s true that Bayern played well. They dominated the ball and the chances created but Madrid – with their noses in front – were in control even without owning possession.

They know what they need to do. More than any other elite team, they are willing to batten down the hatches and suffer. They know that resistance equals success; that if they can’t stop the cross then they can always stop the shot.

“Overall, we have been better than Bayern, we deserved it,” captain Sergio Ramos claimed. “The Madrid DNA pushes you to fight until the end. I’m proud of this team… it’s the reward for so much sacrifice.

“With the score in your favour, unconsciously, you go back a little bit more and the opponent can have more possession. We have been able to get together and suffer together.”

The crucial aspect of Bayern’s failure over two legs is perhaps they didn’t surprise Madrid. Their left wing was beautifully in tandem at the Bernabeu with Alaba and a resurgent Franck Ribery overlapping, dribbling and wreaking havoc in the area occupied by reserve right-back Lucas Vazquez.

From there, there were pull-backs and crosses into the area. But Madrid knew what was coming and dealt with it. And then it became less about the mistakes of the Bayern reserves on the night and more about the inability of their first-choice forwards to convert

Bayern created 20 chances at the Bernabeu and scored twice. Heynckes is right; two away goals should have been enough to see his team through.

But Juventus scored three in the last round and still went out. More is required. Madrid need to be overwhelmed, well beaten, and no team in three seasons has managed to do that to them in Europe under Zinedine Zidane.

But when Robert Lewandowski, in particular, looks back on these two nights, he will see he came up short. Bayern froze in front of goal. The quality of the chances spurned was high; against lesser opposition, in lesser games, he might well have had a hatful. But he could not find his form in the big moments.

He started the season talking about how Bayern would need to spend big money to help him win the Champions League. The next time he feels the club is beneath his standards somebody should clip together his highlights from these two games and ask him to explain himself. Bayern’s top brass have surely learned a lot about their Polish top scorer over the course of these two games.

“Of course we are disappointed,” Alaba told Sky. “It’s difficult to explain why. We know that we missed opportunities and that was one of the reasons.”

This is the end of the line for Bayern. The cannot get past the Champions League semi-finals in their current guise and cannot get past any significant Spanish team for that matter either.

They might well be winning their domestic league by an embarrassingly large margin every season but the current structure and style of the team meets its kryptonite on Spanish soil. There have got to be changes.

Heynckes will go; he is out of contract following his rescue mission and it is sad that he will not depart with the European title. The unproven Niko Kovac comes in.

On the playing front there will be alterations too. Serge Gnabry and Leon Goretzka will come in and have to be accommodated. They are players of promise but Bayern will probably have to aim higher than that if they are to dent Madrid and Barca. Those are Bundesliga-winning signings, not Champions League ones.

Some big starts might well be sacrificed. The injuries at key times to Robben and Boateng could mean that their bodies are no longer capable of lasting a crucial season and all the big moments. Ribery – the best Bayern performer over two legs – is 35 and cannot go on forever.

A more reliable finisher must be sourced; one who is more dead-eye than Lewandowski and calmer in front of the posts than Muller.

From the team which competed in the second leg, who can say they showed what they’re made of? On that basis, Joshua Kimmich, Niklas Sule, Alaba, Thiago and James Rodriguez will be the nucleus to build around; they showed the combination of being on the level and being the right age.

Absentees can be slotted around them but a lot of work needs to be done by Bayern’s sporting director in the next couple of months to ensure they have the squad to go further because Bayern are too good for the Bundesliga and not good enough for their objectives in the Champions League.