Jordaan, who is the president of the South African Football Association, said he was ready to clear his name in court.
"Ms Ferguson has alleged that Dr Jordaan raped her 24 years ago. Dr Jordaan denies that he raped Ms Ferguson," his lawyer, Mamodupi Mohlala-Mulaudzi, said in a statement.
Rapes of women and children are common in South Africa, with women's rights campaigners charging that sexual violence has almost lost the power to shock.
Ferguson, in a blog post last month, accused Jordaan of raping her in 1993 in a hotel in Port Elizabeth on South Africa's south coast after she gave a concert.
Ferguson said she was emboldened to break her silence by the #MeToo social media campaign that grew out of the slew of allegations of predatory sexual behaviour by Hollywood mogul Harvey Weinstein.
Ferguson said that after the concert, Jordaan entered her hotel room and raped her. She said her intention was not to seek revenge.
"The thought of going to the police felt intolerable. What would I say? Should I have screamed louder? Fought him off harder? Had I been complicit in some way?" she wrote. Ferguson said she had not yet decided what legal steps to take.
(Reporting by James Macharia; Editing by Ed Cropley/Mark Heinrich)
