Wilson, 28, won't receive any further pay or benefits, and he and the city have cut their ties, Mayor James Knowles told reporters a day after Wilson tendered his resignation, which was effective immediately.
Wilson, who is white, had been on administrative leave since he killed Michael Brown, an unarmed black 18-year-old, during an Aug. 9 confrontation. A grand jury decided Monday not to indict him, sparking days of sometimes violent protests in Ferguson and other cities.
Wilson wrote in his resignation letter that his "continued employment may put the residents and police officers of the City of Ferguson at risk, which is a circumstance I cannot allow."
His lawyer, Neil Bruntrager, told The Associated Press that Wilson decided to step aside after police Chief Tom Jackson told him about the alleged threats on Saturday.
"The information we had was that there would be actions targeting the Ferguson (police) department or buildings in Ferguson related to the police department," Bruntrager said. He said Wilson, who had worked for the department for less than three years, and the city were already discussing an exit strategy, acknowledging that Wilson staying on as an officer there would be impossible.
Many have criticized the authorities' handling of the case, but Knowles said no leadership changes were in the works. Asked if he would resign, Jackson said flatly, "No."
Benjamin Crump, an attorney for Brown's family, said Wilson's resignation was not a surprise.
"It was always believed that the police officer would do what was in his best interest, both personally and professionally," Crump said. "We didn't believe that he would be able to be effective for the Ferguson community nor the Ferguson Police Department because of the tragic circumstances that claimed the life of Michael Brown Jr."
Crump said the family is still considering civil litigation such as a wrongful death lawsuit, "but don't let that get confused with the fact that they really wanted the killer of their child to be held accountable."
Victoria Rutherford of Ferguson said she believed Wilson should have not only resigned, but been convicted of a crime.
"I'm upset. I have a 16-year-old son. It could've been him. I feel that he was absolutely in the wrong," she said.
Others residents were more sympathetic. Reed Voorhees said he hoped Wilson could find similar work "someplace where he would enjoy life, and move on with his life."
Wilson has spent his career as a police officer, first in neighbouring Jennings, then in Ferguson. Bruntrager said it's all he's ever wanted to do.
"In terms of what it (the resignation) means, it means at this point he doesn't have a paycheque," Bruntrager said. "He has no income so he'll have to make some decisions pretty quickly."
Wilson fatally shot Brown in the middle of a Ferguson street after the two scuffled inside Wilson's police SUV. Brown's body was left for more than four hours as police investigated and angry onlookers gathered.
Some witnesses have said Brown had his hands up when Wilson shot him. Wilson told the grand jury that he feared for his life when Brown hit him and reached for his gun.
The U.S. Justice Department is conducting a civil rights investigation into the shooting and a separate investigation of police department practices. It isn't clear when those results will be announced.
The White House said President Barack Obama will discuss the Ferguson situation Monday with his Cabinet, civil rights leaders, law enforcement officials and others. The meeting will focus on his administration's review of federal programs that provide military-style equipment to law enforcement agencies.
After the grand jury's decision was announced, 12 commercial buildings in Ferguson were destroyed by fire. There have been well over 100 arrests at St. Louis-area protests in that time.
Knowles said there hasn't been a cost assessment of the damage in Ferguson yet, and he promised residents and businesses that the city will do all it can to seek financial help.
"We are committed to rebuilding our city," he said.
Reverberations of the Ferguson events were evident at the St. Louis Rams' game.
Inside the dome, five Rams players engaged in their own apparent show of solidarity for Ferguson protesters, standing with their arms raised in a "Hands Up" gesture before trotting onto the field for pregame introductions. All five — Tavon Austin, Kenny Britt, Stedman Bailey, Jared Cook and Chris Givens — are black.
After the game, about 100 protesters marched in the area near the Edward Jones Dome, chanting, "Ram fans — join the movement." When about three dozen St. Louis officers in riot gear showed up to make sure things didn't get out of hand, many of the fans broke out in spontaneous applause for the officers.