Chief Commissioner Shane Patton said he had advised the Victorian government he would step away from the role "effective immediately".
"It is with a heavy heart that I have made this decision, however I think it is the right one to allow fresh leadership in the role," he said in a statement on Sunday night.
Of the 14,571 Police Association members who took part in the online ballot, more than 12,600 - or 87 per cent - did not have confidence he could lead and manage Victoria Police in the future.
After triggering the events leading to Mr Patton's resignation, police union secretary Wayne Gatt thanked him for his service.
Mr Gatt said the association would now continue fighting to address many of the issues impacting the force, its members, and the community.
Victoria's opposition leader, and former police officer, Brad Battin said a change of leadership wouldn't resolve the systemic issues plaguing law and order in the state.
"The dismissal of the chief commissioner is also not going to change many of the frustrations that our officers are experiencing when the criminals they arrest are released hours later or the resources they need to do their jobs are not forthcoming," he said in a statement.
Victoria's Emergency Management Commissioner Rick Nugent would step into the role "as soon as practicable" until a replacement was chosen, Premier Jacinta Allan said in a statement.
"On behalf of the Victorian people, I thank Shane for his long and decorated service and his leadership through challenging times," Ms Allan said.
Deputy Commissioner Wendy Steendam AM will lead the organisation temporarily.
Both are expected to be considered as possible permanent replacements.
Mr Patton started as a police cadet in 1978 and went on to lead the force through significant challenges including the COVID-19 lockdowns.
His contract was due to expire in mid-2025 and Police Minister Anthony Carbines said earlier in February his contract was likely to be renewed.
The state's top cop had gone to ground since initially vowing to stay on after the union no-confidence vote passed on Friday.
Mr Patton's resignation comes after more than a year of negotiations over a new pay deal for police and three months after he applied to the Fair Work Commission to intervene.
The saga has led to more than a dozen stop-work actions and members rejecting a deal agreed to by their own union, The Police Association of Victoria.
A revised pay deal is set to be put to a vote.
Mr Patton said policing was a "fantastic job, rewarding, challenging" that he would "miss immensely".
He thanked his family and friends for their "love and support over a lifetime of policing" and the Victorian community for "the privilege to have served you".
He also thanked Victoria police and protective services officers, police custody officers and public servants and his executive command team members.
Former chief commissioners Reg Jackson (1971-77) and Mick Miller (1977-87) had no-confidence votes passed against them during their tenures but survived.
Christine Nixon quit as head of the state's bushfire recovery authority following admissions she - as then chief commissioner - left the state control centre and went out to dinner after being told people could die on Black Saturday, February 7, 2009.
Her replacement as top cop Simon Overland resigned in 2011, hours after an ombudsman's report found he was solely responsible for releasing misleading and inconsistent crime statistics before the 2010 state election
10°C