The 34-year-old Divac, who started his career at Partizan before moving to the Los Angeles Lakers in 1989-1990, has run the Belgrade club for four years while also playing for the Sacramento Kings.
He said he was "fed up" with the situation in Serbia-Montenegro basketball, allegedly dominated by "centres of power" and "political games."
Divac left Partizan along with the club's general manager, Predrag Danilovic.
"We are sorry about this, we love this club, but we can no longer stand all those pressures," Divac told a news conference. "We knew that this country was not legally regulated, that there are no laws, but there are limits. Our basketball is ruled by force."
Divac said his club has faced both political and economic pressure, allegedly from rival clubs and a prominent politician. He cited a legal dispute over a player with rival Red Star Belgrade and pressure on Partizan to take part in a regional league as examples of the problems he faced.
"We tried to do things clean, without depending on suspicious people and suspicious money," Divac said. "We no longer want to be part of something that is leading our basketball into a disaster."
Divac recently rejoined the Lakers after six seasons with the Kings.
Divac said he hoped he would play his eventual farewell basketball game with Partizan.