Despite his team routing Tottenham 7-2 in the Champions League in early October, Bayern severed ties with Kovac on Sunday night after winning just three of their last six games.
AFP Sport looks at what prompted the dismissal of Kovac after 16 months in charge:
Lack of boardroom backing
It was no secret that chairman Karl-Heinz Rummenigge was a reluctant supporter of Kovac becoming coach when the former Bayern midfielder succeeded Jupp Heynckes in July 2018.
President Uli Hoeness persuaded Rummenigge that the right man was Kovac, who endured a storm of criticism inside his first three months following back-to-back Bundesliga defeats by Hertha Berlin and Moenchengladbach.
Bayern still won the league and cup double last season, but the writing was again on the wall last month when Hoffenheim pulled off a shock 2-1 win in Munich. Sloppy defending also saw Bayern concede a late goal in their 2-2 draw at Augsburg a fortnight ago.
An unconvincing 3-2 victory at Olympiakos in the Champions League the following game moved Rummenigge to brand the performance “careless”.
“I don’t think the performance we produced will bring us serious success this season,” he said in a thinly-veiled dig at Kovac.
Big name factor
Kovac, after his dismissal, was quoted as saying “this is the correct decision for the club”, and he was never able to allay concerns he was a big enough name for a club of Bayern’s stature.
Following spells under elite coaches in Pep Guardiola and Carlo Ancelotti, Bayern will search for a successor of similar ilk to replace Kovac, whose assistant Hansi Flick will take charge for Wednesday’s Champions League game at home to Olympiakos.
Jose Mourinho has been linked to the role and is reportedly learning German, while Ajax coach Erik ten Hag — Bayern’s reserves coach from 2013-15 under Guardiola — is another contender.
“If Bayern ring, I wouldn’t rule it out,” Ten Hag told magazine Kicker recently.
Ex-Juventus coach Massimiliano Allegri, Ralf Rangnick, director of football at RB Leipzig, and revered former Arsenal boss Arsene Wenger have also been mentioned.
Lost dressing room
Kicker claims Kovac lost Bayern’s dressing room last season and that winning the double only papered over the cracks.
“His concept of football was never clear, players lacked detailed tactical guidance,” Kicker wrote.
What is certainly true is that Bayern’s stars looked desperately short of ideas when Jerome Boateng was sent off after only nine minutes at Frankfurt on Saturday.
Robert Lewandowski bludgeoned his way through the Frankfurt defence for Bayern’s only goal, but individual errors contributed to all five goals they conceded.
Sports director Hasan Salihamidzic says a “positive development” is now expected from the record 29-time German champions “so we can achieve our goals for the season”.
Problems to solve
Kovac’s problems were compounded in recent weeks by losing both first-choice centre-backs Niklas Suele and Lucas Hernandez to long-term injuries.
In Frankfurt, Boateng was paired with David Alaba, usually a left-back, in a curious selection in the middle of the defence.
Boateng is now suspended for Saturday’s home Bundesliga clash against Dortmund with right-back Benjamin Pavard likely to shift into the centre.
Similarly, Kovac’s replacement must solve the same puzzling issue of where to regularly play Thomas Mueller, who made his 500th appearance for Bayern on Saturday yet was frustrated under Kovac by a lack of game time.
Whoever does get the Bayern job, however, still has a good chance of success this season.
Bayern top their Champions League group after three straight wins and are through to the last 16 of the German Cup, while they only trail leaders Gladbach by four points in the league.
