Zuma was deputy president of the ANC and country at the time.
He denied the allegations. He said the sex was consensual and the court acquitted him of rape charges in 2006.
Khwezi, who was HIV-positive, went into exile following the trial after receiving death threats. She later returned to South Africa and died in 2016.
Ramaphosa initially answered the question by saying he had “to go with” the ruling of the court.
He added that he at the same time had to believe Khwezi because of the bravery she showed in coming forward with the rape allegations.
“What the judge said is not a fable. It is the reality that finally led to President Zuma’s acquittal,” he said.