Jupp Heynckes was forced to deny Bayern Munich are bad losers after their shock 3-1 defeat to Eintracht Frankfurt in the German Cup final ruined his final game as manager.

Croatia striker Ante Rebic scored either side of a Robert Lewandowski equaliser before substitute Mijat Gacinovic tapped into an empty net just before the final whistle to delight Frankfurt fans and break Bayern's hearts.

Eintracht coach Niko Kovac claimed his first trophy as a coach in his last match at the club. He is leaving the Frankfurt side to succeed Heynckes at Bayern next season.

However, several Bayern stars left a bad impression by storming off the playing area after receiving their runners-up medals at the Olympiastadion in Berlin.

They broke protocol by not waiting to see Frankfurt lift the trophy and Heynckes was forced to deny the "bad losers" accusations.

"That was really a misunderstanding," insisted Heynckes.

"I would have expected that a person in charge of FC Bayern or the German FA would have told us to wait until the trophy was presented.

"At that moment, I did not even think about it, otherwise I would have asked my team to stay."

Only a few Bayern players lingered for the trophy presentation alongside Bayern's sports director Hasan Salihamidzic.

Nevertheless, the night belonged to Kovac and Frankfurt.

In a dramatic finish, Rebic sealed the win by scoring his second goal on 82 minutes after floating his shot over Bayern goalkeeper Sven Ulreich.

The goal stood despite an intervention by the video assistant referee.

Both Kovac and Heynckes later said Bayern should have been awarded a late penalty when Javi Martinez was fouled in the dying minutes.

"It was a penalty, but we shouldn't start criticising," added Heynckes, while Kovac admitted: "I have to say -- it was a penalty".

However, Gacinovic got the party started for the Frankfurt fans by sprinting the length of the field to tap into an open goal from a Bayern corner for the third goal just before the whistle.

"I'm proud, my boys gave their all -- and I mean all. Now Eintracht can celebrate their first trophy for 30 years," beamed Kovac after Frankfurt's first cup final win since 1988.

The former Bayern midfielder shed tears of joy as he signed off with silverware after two years at Eintracht, who lost last year's cup final to Borussia Dortmund.

"Anyone who knows me knows that I am an emotional person and I let the tears flow. They were tears of relief after two years fighting to be successful again," he said.

"We have continually improved from near relegation to cup final to cup final winners... It's awesome what we have achieved here in the last few years," he added.

"I am just pleased we managed to win it as the underdogs."

This was supposed to be Heynckes' farewell party.

Bayern wanted to send their 73-year-old head coach into retirement with the German cup and league double, having already wrapped up a sixth straight Bundesliga title.

But Heynckes was left lamenting Bayern's wasted chances as both Lewandowski and centre-back Mats Hummels hit the woodwork in either half.

"Congratulations to Eintracht. They played with ambition, were aggressive and hard in the tackle," said Heynckes.

"We lost the ball in a dangerous area (before the first goal) and it was no wonder we fell behind.

"We had a few problems in midweek with Joshua Kimmich and Thomas Mueller both being ill, but that is no excuse... We should have had the ability to win the game."

"It's a pity, but you have to be able to call up your full qualities in a game like this and we didn't manage it," he added.

Frankfurt players interrupted Kovac's post-match press conference by showering him with beer.

"I am happy that we have won the cup after 30 years," said goal-scorer Rebic.

"The team deserves it, Bayern are always the favourites, but at the end... (we) won the cup."