The former midfielder was relieved of his position on Sunday night following a 5-1 drubbing at the hands of Eintracht Frankfurt over the weekend.
Such a result has left Bayern languishing in fourth in the Bundesliga and in desperate need of a big result against the Greek side as a means of restoring some confidence.
Here, Sports Mole looks at how Bayern could line up for the game on Wednesday.
Firstly, with assistant manager Hansi Flick taking over for this game, it can be difficult to know exactly what formation and personnel will be agreed upon, but it is safe to assume that Bayern will want to put out a full strength team as they look to make a statement following Kovac's sacking.
While the selection of Robert Lewandowski, who has 22 goals for club and country this season, is largely obvious, perhaps the most important selection comes with the attacking midfield trio.
Both Serge Gnabry - the hero of that 7-2 win over Tottenham Hotspur - and Philippe Coutinho were withdrawn during the second period against Frankfurt, meaning it is likely that they will start this game, while Kingsley Coman's pace is likely to be preferred to Thomas Muller over on the right-hand side.
Above all, Bayern will not want to find themselves bogged down against an Olympiacos side that is likely to sit back and wait for their moment to counter, which makes picking the quickest possible combination a smart option as the home side targets an early goal.
Further back, Flick is likely to go with most trusted pair of Thiago Alcantara and Javi Martinez, who started in the reverse fixture against Olympiacos and are seen as the duo that brings the most balance, with the former's passing nicely complementing the balancing role played by the latter.
At the back, Jerome Boateng is likely to be used again due to his red card over the weekend ruling him out of Bayern's next domestic game, with the impressive Benjamin Pavard partnering him in central defence.
Although this is not Bayern's strongest central defensive pairing, it enables Flick - like Kovar would often do - to use two positive players in the wide positions - something so crucial when playing against a low block where little space is offered.
The experience of David Alaba on one side will be invaluable, giving Coutinho the licence to stay up the pitch, while Joshua Kimmich has demonstrated on several occasions that his technical skilset enables him to function as more of a right-sided midfielder capable of hitting accurate long shots as well as clearing loose balls at the back.