Without doubt the biggest losers of the managerial appointment, Eintracht Frankfurt have lost a promising manager that had transformed the club in a two-year spell.
But, there is the risk that their final weeks of the season could see a downturn in form as Kovac's mind begins to shift towards Bayern - who Frankfurt could go up against in the DFB-Pokal final should they win their respective semi-finals.
He has signed a three-year contract and will take up his new role on July 1. "We are convinced that he is the right coach for the future of FC Bayern".
Kicker magazine reported that Bayern would pay a fee of 2.2 million euros ($2.7 million) to trigger a release clause in Kovac's existing contract with Frankfurt.
Bobic said Bayern's announcement about Kovac was a surprise, and the timing was detrimental to his current club at the decisive stage of the season.
Several high-profile coaches, including Tottenham boss Mauricio Pochettino, were linked with the Bayern job after Heynckes reportedly rejected the offer of a contract extension.
After the end of his playing career Kovac was briefly an assistant coach in Austria. But his role at the club could take a positive turn under Kovac next season.
"Very annoying, unprofessional and lacking in respect", Bobic said of Kovac's switch being made public.
Eintracht Frankfurt's line-up in 2017/18 based on average position and minutes played. "Bayern have thought of themselves and not for a second about Eintracht Frankfurt".
Heynckes returned in an interim capacity - his fourth time in charge of Bayern, with the previous three reaping a Champions League title as well as four Bundesliga crowns and a DFB-Pokal - in October 2017 after Carlo Ancelotti was sacked.
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.
Bayern was initially in talks with former Borussia Dortmund coach Thomas Tuchel, but he informed the club that he had agreed to take over another team while it was still trying to convince Heynckes to stay.