"President Ramaphosa is not resigning based on a flawed report, neither is he stepping aside," Magwenya said.
Ramaphosa has been under fire since June, when a former spy boss filed a complaint with the police alleging that the president had hidden a February 2020 burglary at his farm in northeastern South Africa from the authorities.
He allegedly organised for the burglars to be kidnapped and bribed into silence.
Ramaphosa has denied any wrongdoing.
But the scandal, complete with details of more than half a million dollars in cash being hidden under sofa cushions, has come at the worst possible moment for him.
On December 16, Ramaphosa contests elections for the ANC presidency -- a position that also holds the key to staying on as national president.
"The president has taken to heart the unequivocal message coming from the branches of the governing party who have nominated him to avail himself for a second term of the leadership of the ANC," Magwenya said.
"The president understands that message to mean he must continue with both the state and economic reforms," he added.
"The president has with humility and with great care and commitment accepted that call to continue being of service to his organization the ANC and to the people of South Africa."