Thursday's 1-1 draw which sealed Partizan's berth was not enough to save Djukic, who paid the price for being comfortably beaten to the league title by rivals Red Star Belgrade last season and overseeing a disappointing start to the new campaign.
"The club's managing board reached a unanimous decision at Friday's meeting to part ways with Miroslav Djukic by mutual consent," Partizan said in a statement.
"We thank Djukic for his professional conduct and commitment to the club, wishing him all the best in his future endeavours."
Mirkovic, who won three league titles with Partizan in the former Yugoslavia, is set to take on his first job as head coach at any level after a stint as assistant to Montenegro boss Ljubisa Tumbakovic.
Djukic came under pressure last season despite winning the Serbian Cup and reaching the Europa League knockout stages after finishing a distant second to champions and bitter city foes Red Star in the league.
Fan discontent culminated after a 1-0 league defeat at nondescript Radnik Surdulica on the opening day of the season and a fortuitous 1-0 first-leg Europa League win over Trakai.
Partizan meet Danish side Nordsjaelland in the competition's third qualifying round, with the first leg in Denmark on Aug 9.
(Writing by Zoran Milosavljevic; Editing by Christian Radnedge)
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