The teen does not remember if they had sex, but the man's semen was found on vaginal swabs taken from the complainant.
The man claimed they were interrupted before they had sex.
The Court of Appeal earlier dismissed the man's appeal based on the fact that the swabs did not prove any direct evidence of penile penetration - needed to prove rape - and that the semen could have arrived there by some other way such as a finger.
In its judgment, the Court of Appeal found that the swabs were a powerful piece of circumstantial evidence when combined with other evidence at the trial and had been "squarely before the jury" to decide.
In his latest application, Herbet argued leave should be granted because of the court's approach to scientific evidence which affected the reasonableness of verdicts.
But the Supreme Court sided with the Court of Appeal and found nothing raised by Herbert led to an appearance of a miscarriage of justice and that the jury was entitled to include the scientific evidence to help it settle on a verdict.
"There is no challenge to the principles applicable to unreasonable verdicts," the ruling said.
The application for leave to appeal was dismissed.