Bayern sports director Hasan Salihamidzic said, "we lost to Real previous year and meant to do better this time".
"You saw yesterday in Manchester and Rome that we can't underestimate any team - all the three other teams are at the top level", he said. "We are convinced that he is the right coach for the future of FC Bayern".
Heynckes called Kovac "ready for Bayern as he knows the club and has gained experience working for several clubs and the Croatian national team".
At a news conference later Friday, the older Kovac said he had mixed feelings about leaving Frankfurt, but "not many coaches, not many players" get an opportunity at Bayern.
Efforts and strategies are being put in place to see that the club keeps Heynckes' assistant, Peter Hermann and keep Kovac's brother, Robert as assistant coach as well.
Heynckes was only tempted out of retirement in order to help Bayern after they sacked Carlo Ancelotti last October. "I think Bayern Munich made a good choice".
Having taken over in March of 2016, he saved Frankfurt from relegation, and in the following season itself, was able to guide them to the finals of the German Cup.
The club issued a press release on Friday.
Bayern grew more and more frustrated as the game went on, Robben spurning a number of opportunities in the second half.
"They will most likely make the Champions League this season, or if not at least qualify for Europe".
Bayern prevailed in 2012 in a penalty shoot-out, but in both 2014 and previous year it was Real who prevailed and they look well poised to make it a hat-trick this time around.
Frankfurt can still win a title this season as Kovac's men clash with Schalke in the German Cup semi finals on Wednesday.
"The coach keeps the team together brilliantly". According to several media reports, the German is destined for Paris St Germain for the next season.
Tottenham Hotspur's Mauricio Pochettino, Lucien Favre, now at Nice, and RB Leipzig coach Ralph Hasenhuettl were also at times named as possible Bayern coaches.