He had been on life support in hospital since the shooting on November 15.
Police say that Jamar Clark was the suspect in an assault case and was interfering with medics who were working on the victim when he was he was shot.
Protesters have camped outside the police station for two days, and blocked a major highway on November 16.
That demonstration led to the arrest of 51 protesters on that night.
Police have released few details about the shooting of Jamar Clark – who some say was handcuffed when he was shot. Police have denied that claim.
The demonstrations came after the mayor’s decision to ask the federal government to launch a civil rights investigation.
Mayor Betsy Hodges said she was asking for the investigation in the “interest of transparency and community confidence”.
While a state agency has already launched a criminal investigation, the mayor said that Minneapolis needs “all the tools we have available to us”.
Two officers involved in the shooting are on paid leave – which is standard procedure after incidents such as this.
The police chief has said that the officers were not wearing body cameras, but would not say whether the squad car or other surveillance video captured the incident.
Protesters have welcomed the federal investigation, but have vowed to continue demonstrating until any video of the situation is released and the officers involved are identified.
The protests began on November 15 and included an overnight encampment at a Minneapolis police station near the scene of the shooting.
At least eight tents were seen at the campsite on the next day, and a few protesters were sitting inside the glass doors of the station – including one who was knitting.
“We’re still not moving until we get that footage,” said Michael McDowell, a demonstrator with the Black Lives Matter movement.
According to police, the incident began on November 15 when police were called to north Minneapolis following the report of an assault.
At the scene, police found Jamar Clark interfering with paramedics who were attempting to help the victim. They attempted to calm him, which resulted in a struggle and a shot being fired, police said.
Jamar Clark’s father told the Associated Press news agency that his son suffered a single gunshot wound over his left eye.
His brother told the AP that family members assembled at the hospital on November 16 to take Jamar Clark off of life support.
A number of high-profile police shootings of black people have sparked protests nationwide about the police use of excessive force against African Americans.
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