Michael Phillips, 57, who is now in a nursing home because of sickle cell anemia, spent 12 years in prison for the crime. He was jailed for another six months after his release because he failed to register as a sex offender.
Phillips is believed to be the first person in the United States cleared by DNA without requesting a test.
"I never imagined I would live to see my name cleared," Phillips said in a statement given through the Dallas County District Attorney's Office. "Six of my siblings died from the same disease, so I think God for sustaining me in prison. I always told everyone that I was innocent and now people will finally believe me."
Craig Watkins, who has been district attorney since 2007, set up a conviction integrity unit. The mismatch in the Phillips case came up during a systematic check of evidence from some 1990 rape cases.
"DNA tells the truth, so this was another case of eyewitness misidentification where one individual's life was wrongfully snatched and a violent criminal was allowed to go free," Watkins said. "We apologize to Michael Phillips for a criminal justice system that failed him."
Another man, Lee Marvin Banks, who lived in the same Dallas motel as Phillips and the victim, was linked to the rape by DNA, Watkins said.
Phillips is expected to get a lump-sum payment from the state of Texas and an annuity.