The vote in the St Louis suburb is the first since the death of Michael Brown last August led to protests.
A federal investigation found racial bias in the Ferguson police department was widespread.
Two-thirds of Ferguson's residents are black and now half the council.
Shortly after the results came out, a video emerged showing an unarmed black man being shot dead by a police officer in South Carolina.
State investigators said the officer, Michael Slager, would be charged with murder after the video showed him firing at Walter Lamer Scott who was running away.
Turnout in Ferguson increased from 12% at the last elections, in 2013, to 29%.
Wesley Bell, who defeated another black candidate in Ferguson's third ward, said: "This community came out in record numbers to make sure our voices were heard.
"When you have a community engaged, the sky is the limit."
A drive by activists to register new voters and encourage previously disenfranchised residents to vote appeared to have paid off.
"People in general want to see change," Ferguson Mayor James Knowles told the Reuters news agency.
Ella Jones defeated another black candidate and two white candidates in Ferguson's first ward to become the first black woman on the council.
Black residents in Ferguson protested for several days last August after Mr Brown was shot dead by St Louis police officer Darren Wilson.
The protests spread nationwide in November when it was announced that Mr Wilson, who has since left the police, would not be charged.
US police have faced severe criticism from rights groups in the wake of Mr Brown's death, with a series of high-profile deaths of unarmed black men in police custody.
Voters in Ferguson, Missouri, where last year an unarmed black teenager was shot dead by police, have tripled the number of African-Americans on the six-member council from one to three.