Two international stars -- Real Madrid midfielder Luka Modric and defender Dejan Lovren -- appeared as witnesses during the trial in Osijek providing details of their transfers from Dinamo.
The players' evidence came under official scrutiny.
Croatia captain Modric was charged in March for alleged false testimony over the details of his 2008 transfer from Dinamo to Tottenham Hotspur.
Lovren, questioned over his 2010 transfer from Dinamo to French side Lyon, was also investigated.
Mamic, 58, was not present at the tribunal in the eastern town of Osijek for sentencing. He travelled to neighbouring Bosnia on Tuesday claiming he was not on the run but wanted to avoid "frustration" at the court.
"I went to find peace," Mamic, who also holds Bosnian passport, told local media late Tuesday from Medjugorje, a southern Bosnian town famed for alleged apparitions of the Virgin Mary.
"I can return whenever I want."
Mamic is considered the most powerful figure in Croatian football and his trial, that opened in April 2017, was a further problem for a sport already struggling with hooliganism and poor infrastructure.
He was tried along with three others -- his brother and former Dinamo Zagreb coach Zoran Mamic, former club director Damir Vrbanovic, and a tax inspector.
According to the indictment, the corruption cost Dinamo more than 15 million euros ($18 million) and the state 1.5 million euros as cash was embezzled through fictitious deals related to player transfers.
Judge Darko Kruslin found all four defendants, none of whom was present on Wednesday, guilty.
"Zdravko Mamic is sentenced to a total prison sentence of six years and six months," Kruslin said.
The verdict is not final, but, under Croatian law a person sentenced to more than five years in jail must go to prison immediately.
Vrbanovic, also a top Croatian Football Federation official, and Zoran Mamic were sentenced to three years and four years and 11 months in jail respectively.
The tax inspector was jailed for four years and two months.
The trial was held in Osijek because Mamic allegedly has close ties with some judges in Zagreb.
All four defendants pleaded not guilty.