Bayern's sporting director Hasan Salihamidzic said despite losing to Real in the 2017 quarter-finals, they held no fear for the Bavarians. "We're convinced he's the right coach for the future of FC Bayern".
The 46-year-old Croatian will get a three-year contract from July 1, said the club, just minutes before Friday's Champions League semi-finals draw which left the Bundesliga champions pitted against defending champions Real Madrid.
Kovac will be joined at Bayern by his younger brother Robert, who also acts as his assistant in Frankfurt.
They are attempting to be the first club to win the competition in three consecutive seasons since Bayern won it a third time in 1976.
Kovac captained Croatia towards the end of his playing career and his brother took over the armband when Niko retired from worldwide football.
Sandro Wagner scored a quickfire double as a much-changed Bayern Munich came from behind to kick off Jupp Heynckes' farewell matches with a comfortable 5-1 Bundesliga victory over Borussia Monchengladbach.
Yes, in the social media-driven world that we now live in, where team's compete to unveil new signings in the most freakish ways imaginable, the German league have went back to basics with this portrait of Kovac.
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"There was no contact".
"I've seen them about six times this season and they've been all over the place defensively, especially when they played Tottenham". Bayern have thought of themselves and not for a second about Eintracht Frankfurt.
The win cements Leverkusen's grip on fourth place and gives them a five-point cushion over Hoffenheim, in fifth, and Frankfurt, who are in the Europa League places. It's annoying we must talk about this.
The veteran coach has since backed Kovac to continue his work in the new campaign and is quoted by Daily Mail as saying: "Kovac generally makes a very positive impression".
Frankfurt had learned the day before that its coach, Niko Kovac, is leaving for Bayern Munich next season. It allows him to leave "for a big European club" for 2.2 million euro.
He had brought Frankfurt back from the brink of relegation during the 2015-2016 season.
"He has a very, very good CV as a coach". And he worked with a lot of different personalities and nationalities at Frankfurt. 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.