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The Croatian - who has been both a manager and director of football at Dinamo - has been sentenced for fraud and embezzlement. Mamic's brother Zdravko, Dinamo's former executive director, had his sentence confirmed by the court, as did Damir Vrbanovic and Milan Pernar.
The four men had been charged with tax evasion worth 12.2 million kuna (around £1.4 million) and for siphoning off 116 million kuna (£13 million) from the transfers of players from Dinamo.
"Although I don't feel guilty, I resign as I said before I would do if the sentence was confirmed. I wish all the good luck to the club," the departing Mamic said in a statement.
The manager's brother, Zdravko Mamic, originally fled across the border to Bosnia to hold a press conference at a five-star hotel, before giving himself up to police.
Former Dinamo player Damir Krznar is stepping in to take over as head coach, but he has a matter of days to prepare for the visit of Tottenham in a Europa League last-16 second leg on Thursday.
A Harry Kane brace in the first leg gave Tottenham a 2-0 win in London. And, if Jose Mourinho's side weren't already favourites to go through, they might fancy their chances even more strongly now that the 21-time Croatian champions have been plunged into chaos.
The 49-year-old Mamic has won four Croatian First League titles over two stints as manager of Dinamo Zagreb, the club where he also spent much of his playing career. But he now faces a battle to save his reputation within the game.
"The Supreme Court has confirmed the Osijek Municipal Court's verdict sentencing Zdravko Mamic to six and a half years of imprisonment for the embezzlement of 116 million kuna from Dinamo football club," read a statement published by Croatian outlet HRT.
"Zoran Mamic's sentence has been reduced to four years and eight months from four years and 11 months, while Milan Pernar had his sentence reduced to three years and two months from four years and two months."
All imagery: PA Images