The 72-year-old will end his third spell in charge of the club this summer and there has been much discussion surrounding who will take over at the end of the season.
Eintracht Frankfurt sporting director Fredi Bobic was not willing to ascribe such values to Bayern Munich at a press conference on Thursday following the announcement.
The 46-year-old will start a three-year contract with Bayern from July 1. "Niko was a player at Bayern, he knows the characters and the structures and the DNA of the club very well".
Bayern sports director Hasan Salihamidzic said, "we lost to Real a year ago and meant to do better this time".
He learnt to play football in the concrete cages of the capital, where he developed the technical ability and physical toughness that later saw him make 379 Bundesliga and 2.Bundesliga appearances for Hertha Berlin, Bayer Leverkusen, Hamburg and Bayern Munich, with whom he won the league in 2003.
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Kovac, a former Croatia midfielder and coach, played for Bayern between 2001 and 2003, winning the Club World Cup in 2001 and a domestic league and cup double in 2003.
Kovac will be joined at Bayern by his younger brother Robert, who also acts as his assistant in Frankfurt. "I think Bayern Munich made a good choice". The former striker has won the Europe's premier club prize as a coach with both clubs (1998 with Real and 2013 with Bayern). "It's hard for me now that it's ending soon". They play husLiverpool have been drawn against Roma in the semi-finals of the Champions League.
One man who his side will have to keep a close eye on is the red hot Cristiano Ronaldo, who has scored in every single game of the competition this season. "It's unfortunate timing. The fact that information surfaced yesterday not from Frankfurt but from Munich is aggravating, unprofessional and is lacking respect". "They only thought about what served them best but did not regard what would be good for Frankfurt. In football, you always have a chance as you saw in the Champions League in midweek".
The defending champions had a 6-3 aggregate win against their German counterparts in the quarter finals playing a 2-1 first leg away win and another 4-2 spanking at the Bernabeu last season.
Kovac is described as a team player, addressing the need to get along with the club's leaders. "Colombia could do well too because they've got some great players".