It is the latest in a series of protests that erupted across the US after a grand jury last week decided not to indict white police officer Wilson for killing Brown on August 9.
Wilson wrote in his letter "it is my hope that my resignation will allow the community to heal".
But dozens of demonstrators again gathered outside Ferguson police station despite his decision to quit, with protesters setting fire to a US flag and jeering at police officers.
One man, who gave his name as "Kenny," said: "I'm mad as hell. Every night we're going to be here."
There was also a brief standoff outside a bar between demonstrators and riot police before organisers moved protesters along.
The grand jury decision revived long-standing questions about how police, especially white officers, interact with African Americans - questions raised again after last week's shooting in Cleveland of 12-year-old Tamir Rice.
Watch: Car crashes Into Minneapolis protesters
"What we're endeavouring to do here is seek justice for a grieving family as well as systemic, fundamental reform in terms of policing," Brooks said. "When you have a 12-year-old child who is killed with a toy gun in his hand, there is something fundamentally wrong."
Yesterday hundreds of protesters demonstrated in and around Washington, including laying on the ground for several minutes in a "die in" at an area shopping centre.
The NAACP's demands include requiring police to use body cameras, reforming the system of equipping police with military hardware, promoting diversity on the force and ending the use of serious force in cases involving minor offences.
"I served my country. I spent four years in the army, and I feel like that's not what I served my country for," said Ebonie Tyse, 26, of St Louis, as National Guard and police vehicles roamed the street. "I served my country for justice for everyone. Not because of what colour, what age, what gender or anything."
- AFP
