Treatment of the youths known as the Scottsboro Boys - nine in all - helped spark the US Civil Rights movement.
The boys were convicted by all-white juries.Eight were sentenced to death but none was ever executed. Five of the boys' convictions were overturned, and a sixth was pardoned in 1976.
The decision by an Alabama parole board is the last chapter in a case that came to symbolise racial injustice in America's deep south, says the BBC's Jane O'Brien.
"While we could not take back what happened to the Scottsboro Boys 80 years ago, we found a way to make it right moving forward," said Alabama Governor Robert Bentley. "The Scottsboro Boys have finally received justice."
In March 1931, during the Great Depression, the boys were travelling by train through northern Alabama among a group of hobos, both black and white.
A fight broke out and the train was stopped near the town of Scottsboro. Nine black teenagers ranging in age from 13-19 were arrested.
"The deputy sheriff realised two of the white hobos were in fact women," historian Dan Carter told the BBC in October. "The young women worried they might be accused of prostitution, so they accused the black boys of having raped them.
"I think anyone today who studied the evidence would conclude no rapes occurred."
Great day for freedom'
Charles Weems, Andy Wright and Haywood Patterson were pardoned on Thursday by the Alabama Board of Pardons and Paroles (ABPP).
Convictions against Olen Montgomery, Ozie Powell, Willie Roberson, Eugene Williams and Roy Wright were overturned and charges dropped in 1937.
Clarence Norris received a pardon from Alabama Governor George Wallace in 1976. Norris, the last surviving Scottsboro Boy, died in 1989.
Civil rights groups' efforts to fight their convictions and to win new trials sparked civil rights protests and led to two landmark US Supreme Court rulings.
The US high court overturned convictions for some of them in 1932 on the grounds that the teenagers were denied competent legal counsel, and again in 1935 because African Americans were not allowed to serve as jurors during the trials.
The Alabama state legislature passed a law earlier this year allowing the parole board to grant the Scottsboro Boys posthumous pardons.
"Today, we were able to undo a black eye that has been held over Alabama for many years," ABPP assistant executive director Eddie Cook said following the board's unanimous decision.
The men's struggles later inspired books, films and a Broadway musical, as well as the Scottsboro Boys Museum and Cultural Center.
"It is a great day for freedom," the museum's executive director Shelia Washington said.
