Kovac is a reactive coach who has started with no fewer than seven different formations in his 30 Bundesliga games this term - something that should appeal to Bayern given the sheer breadth and depth of abilities in their squad; but the Berlin-born former Croatia worldwide still has certain predilections.
Here are three winners and three losers.
Bundesliga champions Bayern Munich eased past Borussia Monchengladbach after recovering from falling behind to beat their opponents 5-1 on Saturday. "I hope that's a good omen".
The announcement has left Bobic furious, especially with regard to its timing.
"It's a good choice". But his role at the club could take a positive turn under Kovac next season.
They were rewarded with the lead as Drmic cut inside and finished with aplomb as Bayern laboured following their Champions League exploits.More news: Unnao rape case: Zero tolerance against corruption, crime: Yogi Adityanath
Frankfurt's head coach Niko Kovac.
After former Dortmund coach Thomas Tuchel rejected an offer, announcing he will join a big European club overseas.
"We're very happy that we could win Niko Kovac as a new coach for Bayern", sports director Hasan Salihamidzic said. "Bayern have thought of themselves and not for a second about Eintracht Frankfurt". "One has to accept that, but it's not a problem for us".
The club's resurgence has continued this term with Kovac's men fifth in the Bundesliga, just two points behind Bayer Leverkusen, who occupy the final Champions League qualifying spot.
Lewandowksi came off the bench to get on the scoresheet himself, his 27th Bundesliga goal of the season taken well in the closing stages as Bayern racked up a 15th league win from their last 17 outings.
Kovac will be joined at Bayern by his younger brother Robert as assistant coach.More news: Israeli security heads confer after Trump's threat to bomb Syria
Set to return to Real when the 2018/19 campaign is over, James had expressed his desire to stay in Germany past his loan deal. According to several media reports, the German is destined for Paris St Germain for the next season. Right now or at the end of the season, which would have been possible, then we said: If we were in their situation, we would also be interested in finding out as soon as possible that our coach will be lost.
In recent weeks, Hoffenheim manager Julian Nagelsmann's name has been thrown into the hat for the Bayern Munich job, especially following Thomas Tuchel turning the role down.
"It's not so simple, I have to admit", Kovac said.
But now the dream of managing Bayern is over, for the time being at least.
"The coach keeps the team together brilliantly".More news: North Korean leader meets senior Chinese official