Chief Tim Gannon and Officer Kim Potter have quit the Brooklyn Center force.
Mrs Potter said she shot Daunte Wright accidentally, having mistakenly drawn her gun instead of her Taser, a stance backed by Mr Gannon.
Despite the resignations fresh clashes between police and protesters erupted for a third night.
Mr Wright’s mother has been speaking about her last phone call to her son. In tears, she told reporters she could never have imagined he would be killed.
The death happened in a suburb of Minneapolis, a city already on edge amid the trial of a white ex-police officer accused of murdering African American George Floyd.
On Tuesday night bottles and other projectiles were thrown at the Brooklyn Center police headquarters and officers responded by firing tear gas, stun grenades and rubber bullets.
More than 60 people were arrested, Minnesota State Patrol Colonel Matt Langer told reporters.
Another demonstration broke out in Portland, Oregon, on Tuesday night, with about 100 protesters marching on the Portland Police Association Building.
Flames were seen coming out of the side of the police building about an hour later. The Portland Police Bureau declared the gathering a riot.
Portland was the centre of mass demonstrations last year, in the wake of the killing of George Floyd.