With Kovac now confirmed to take over Bayern from July, James' potential future with the club may be thrown into doubt - which would not be a good thing for either party. Real Madrid and Bayern Munich will meet in the Champions League semi-final and Colombia worldwide James Rodríguez is on loan at Bayern from the LaLiga side.
"We are very happy that we can have Niko Kovac as the new coach of FC Bayern".
The Frankfurt coach said his move would have "no influence" on the team's remaining games of the season.
Salihamidzic said: "We agreed a three-year contract on Thursday".
"Thomas Tuchel told us that he's signed with another club".
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Kovac's brother Robert, also a former Bayern player, will join him from Frankfurt as his assistant.
Bayern have won four of the six previous last-four ties between the two clubs, starting with a 3-1 aggregate victory when the clubs first met in 1976. In 2013 as he was set to retire for the first time, Bayern announced Pep Guardiola before the season was over and Heynckes bowed out in the best way possible - with a treble.
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. "Everyone respects the other", Frankfurt forward Kevin-Prince Boateng said earlier this season.
Heynckes took over following ex-Chelsea boss Carlo Ancelotti's dismissal in September and led Bayern to their sixth Bundesliga title in a row. "Sure they have great players, but so do we", Heynckes said.
Bayern' s latest coaching appointment has caused criticism from Frankfurt sports director Fredi Bobic who accused Munich of not acting entirely professionally.
Kovac, like James, was a serial victor as a player.