Harris County District Attorney Patricia R. Lykos said the ruling fully clears 50-year-old George Rodriguez and "justice has been done."
Prosecutors say DNA tests found on hairs at the scene prove Rodriguez did not commit the crime.
Rodriguez has been free since a court ruled in 2004 that faulty evidence was presented at trial.
Test results verified that the girl's abduction and sexual assaults was committed by two other men.
One of them, 50-year-old Manuel Beltran is serving a 60-year prison term for those offenses. The other, who was never charged, is now deceased.