Charlie Robertson, 68, had faced life in prison before his acquittal by the all-white jury.
The former mayor and two other men were tried in the death of Lillie Belle Allen, a preacher's daughter from Aiken, S.C., who was gunned down by a white mob on July 21, 1969. The other men were convicted of murder and face a maximum sentence of life in prison; jurors had the option of convicting them of manslaugter.
The long-unsolved case is nearly finished: Of the 10 white men charged in Allen's slaying, six pleaded guilty earlier and await sentencing. The final suspect faces trial later.
Earlier, the jurors appeared to be divided on whether to convict the three men, asking the judge whether it was too early to declare a hung jury.
"If you have to inquire, it probably is," Judge John C. Uhler told them before he sent them back to deliberate.
Robertson, the city's former mayor who was a policeman at the time of the riots, is accused of inciting white gang members and handing ammunition to at least one shooter.
A second defendant, Robert Messersmith, allegedly fired the fatal shot at Lillie Belle Allen on July 21, 1969, while Gregory Neff is accused of firing three times at Allen's vehicle. None of the defendants testified.
The jury, which began deliberations Thursday, returned three times Friday and twice on Saturday morning with questions for Uhler. He denied their requests to review testimony, but went over aspects of the law with them.
Jurors have appeared tired, sometimes closing their eyes or rubbing their temples while listening to the judge.
Allen, 27, of Aiken, S.C., was shot to death after she got out of her family's white Cadillac to try to help her panicking sister steer the stalled vehicle away from a mob of armed white gang members.
The attack was one of scores during 10 days of violence between blacks and whites. More than 60 people were injured and whole blocks burned before hundreds of National Guard and state police quelled the violence.
In final arguments Thursday, prosecutors said police whipped white youths into a racist frenzy before Allen was ambushed. Defense attorneys said incriminating testimony was unreliable and "bought" with plea deals.
Jurors can convict all three men of first-degree murder, which carries a life sentence; or second-degree murder, which carries a sentence of 10 to 20 years. They also could convict Messersmith and Neff of voluntary manslaughter, which carries a sentence of six to 12 years.
Prosecutors reopened the case in 1999, saying that witnesses were coming forward with new information because of news stories about the 30th anniversary of the riots.
Nine white men were arrested last year in the case; six pleaded guilty. Another man was arrested in July and is to be tried separately. Two black men also face trial; they are accused of the slaying of a white patrolman during the riots.