As the final whistle sounded, the Weser-Stadion was boiling over. The deafening noise was a mixture of fury, disbelief, and anguish. 

Referee Daniel Siebert and his officials were jeered from the pitch, Bayern coach Niko Kovac faced similar barracking and his players were pelted with beer as they tried to celebrate with their fans in the away end.

All thanks to a contentious penalty call around the 80th minute when Kingsley Coman went down following a tussle with Theodor Gebre Selassie.

"If you don’t use VAR, you may as well get rid of it," Max Kruse fumed at the final whistle.

With 40,000 irate, whistling Bremen fans raining down upon him, Robert Lewandowski kept his cool from the spot to seal Bayern a 3-2 win and a place in the German Cup final. 

The defining moment of the match might even have saved Kovac from an end-of-season trip to the nearest job center.

Comeback out of the blue

Leading into the 74th minute, however, Bayern appeared home and dry and in no need of a slice of luck.

Goals from Lewandowski and Thomas Müller either side of halftime had nullified a spirited performance from Bremen and paved the Bavarians' way to Berlin.

But Bayern's defense has been a glaring weak link this season as former world beaters Jerome Boateng and Mats Hummels decline with age. And it once again reared its decaying head on Wednesday night.

Hummels was turned inside-out on the edge of the box in the 74th minute, as Bremen’s dangerman Milot Rashica crossed low for Yuya Osako to fire home.

And one minute later, Rashica broke away from near the center of the pitch, streamed towards the right, left Hummels stumbling, and fired hard and low past Sven Ulreich for the equalizer. 

The two lightning-quick goals sent the Weser-Stadion into delirium and threatened to derail Bayern's topsy-turvy season once again, only for the late penalty drama to come to the rescue.

VAR controversy

Bremen’s players were livid at the final whistle, questioning why the video referee hadn't intervened. The official call was that a clear and obvious error hadn't been identified.

“I don’t think it was a penalty; it's unfair, I can't process it. It's just a bad call from the referee,” Max Eggestein lamented. "And that the VAR saw no problem with it, is just unfair. You can feel it now in the dressing room. It hurts."

It will take Bremen a while to recover from this blow, especially as victory would have sealed Europa League qualification. Now they’ll have to navigate their way back into Europe the hard way — in the closing Bundesliga matches of the season.

But the players can hold their heads high. Coach Florian Kohfeldt once again proved his tactical nous as Bremen controlled large periods of the game and had Bayern rattled at times. Max Kruse’s deployment as a roving midfielder particularly threw Kovac's men off balance.

A common theme in German football prevailed, however, as the 28-time Bundesliga champions and 18-time Cup winners ironically got the rub of the green in Bremen.

Kovac on track

"What others dream of, we live," read a banner from Bayern's away fans after the final whistle.

It was a brutal dig at their opponents but an accurate, and perhaps prophetic, reading of the landscape in German football.

This will be Bayern’s 11th final in 17 seasons and Kovac's third consecutive appearance in the Berlin showdown — having taken former club Eintracht Frankfurt there twice in a row. The Croatian is under intense pressure to deliver silverware in his first season but he's still on track for the double.

"It was a great football game, but we deserved the win because we had the better chances than Bremen," he said in the post-match presser.

Bayern now roll on towards Berlin and a clash with RB Leipzig. The scene for glory is set, but questions about a fragile defense still remain unanswered and could still curtail Kovac's reign in Munich.