DNA testing was not available at Arthur Mumphrey's 1986 trial for the rape of a 13-year-old girl, but recent tests requested by his attorney showed Mumphrey's blood and saliva samples did not match stains on the victim and her clothes.
"Because of technology we have now, justice was not done 20 years ago," State District Judge Kathleen Hamilton said.
Mumphrey, 42, had been sentenced to 35 years in prison.
Prosecutor Marc Brumberger apologized to Mumphrey. "We feel terrible about what happened to you," he said.
Mumphrey's brother, Charles, confessed to the rape this week while serving time in jail for unauthorized use of a motor vehicle.
He is unlikely to face charges in the sexual assault because the statute of limitations has expired, but the information could be used against him in sentencing if he is convicted of another crime and if DNA results support the confession.