The results from the new testing earlier this year found that DNA on the victim's clothing did not match James Calvin Tillman's genetic profile, contradicting circumstantial evidence that had been used to convict him in 1989.
He had been sentenced to 45 years in prison.
Judge Thomas Miano dropped all charges against Tillman during a brief hearing Tuesday and said the case highlighted a need for prosecutors to take extra care to avoid wrongful convictions.
Tillman, 44, talked to reporters outside the courthouse with his mother and brother by his side. He said he wasn't sure what he would do now that he is free.
"I don't hate nobody, I can't live my life hating nobody," Tillman said.
He was 26 and living in a homeless shelter when he was charged with abducting a woman as she got into her car near a Hartford restaurant, then beating and raping her at a nearby housing project.
Tillman maintained his innocence and rejected a plea bargain that would have given him eight years in prison.
The victim had picked him out from a series of photos, and forensic tests at the time showed some similarities between Tillman's DNA and that of the attacker. However, more sophisticated DNA tests conducted earlier this year at the request of the Connecticut Innocence Project categorically ruled out Tillman as the source of the DNA.
Tillman's mother, Catherine Martin, had visited him in prison every week until he was released June 6. She and her son sang gospel songs to each other through the clear pane that divided them.