The Croatian champions announced that Jakirović’s assistant, Sandro Perković, will step in as the interim coach. Dinamo is set to face Monaco at home in their next Champions League match in two weeks.
Bayern made history by becoming the first team to score nine goals in the Champions League since the tournament's rebranding 32 years ago, with Harry Kane netting four goals, three of which were penalties.
Dinamo found themselves trailing by three goals at halftime but managed to score twice within a minute to narrow the gap to 3-2 shortly after the break, only to see their defense falter in the second half in Munich.
While several teams have scored at least 10 goals in a match during the European Cup era, Feyenoord holds the record with a 12-2 victory over KR of Iceland in the 1969-70 season.
Jakirović, who represented Bosnia-Herzegovina as a player, had been at the helm of Dinamo for 13 months, leading the team to a domestic league and cup double last season.