However, at current side Frankfurt the tactically astute 46-year-old has forged a reputation as one of the most sought-after coaches in Germany's top-flight - see above video for a more in-depth look at Kovac's Frankfurt - and reaction to the appointment has on the whole been very positive.
Bobic also spoke about the exit clause that was triggered by Bayern, saying: 'Yes, there was an option for Niko Kovac to get out of the contract if an absolute European top club came.
The Croat, who had also coached his country at the last World Cup in Brazil, had impressed by helping Frankfurt survive relegation in 2016 before leading them to contention for a European slot for next season.
Kovac will be joined at Bayern by his younger brother Robert, who also acts as his assistant in Frankfurt.
"We're very happy that we could win Niko Kovac as a new coach for Bayern", sports director Hasan Salihamidzic said.
"Panita, I wish you the best in your new stage... except when we meet in the Champions League, of course".
Born in Berlin to Croatian parents, both brothers played for the Croatian national team as well as Bayern.
Not to be outdone Lewandowski, sporting a black eye from Wednesday's Champions League clash against Sevilla, came on for Wagner to score Bayern's fifth.
However, Frankfurt football director Fredi Bobic was not pleased that Bayern made the announced before their matches against Bayer Leverkusen and Schalke. "But what do you want, that is how Bayern work, only thinking about themselves". "A huge fixture, in a very positive way", he said.
Thomas Tuchel had been regarded as a frontrunner, before Bayern chairman Karl-Heinz Rummenigge claimed the former Borussia Dortmund boss - expected to replace Unai Emery at Paris Saint-Germain - has agreed a deal with another club.
However, the performance at the BayArena did not back up Kovac's words as Frankfurt's Champions League hopes suffered a heavy blow. With Real looking vulnerable despite Ronaldo's extraordinary performances, Bayern has a chance to provide their coach with the flawless send-off - and even provide a little bit more romance.