"I had no hand in writing the story," Gaye Davis said on Tuesday.
"I did, however, early on Sunday evening, get confirmation from Mr Ramaphosa that – contrary to what the article was stating – he had accepted and signed his nomination form," she said in a statement sent to Sapa.
Davis was stepping down to "publicly disassociate" herself from the Star's article.
"Ethically, I believe I cannot publicly distance myself from the story while remaining in the employ of Independent Newspapers."
Davis believes resigning is necessary to protect her credibility as a journalist.
She told the writer of the article that Ramaphosa had confirmed he was still in the running, but was told the Star was standing by their story, but that other editors in the group could make their own judgments.
"I communicated with the other morning newspaper editors in the group, who took appropriate action and did not run the story in its original form," Davis said.
Independent Newspapers chief executive Tony Howard said he only just learned of the resignation and could not yet comment.
Davis had been group deputy political editor since October 2008. She said she contacted Ramaphosa and personally informed him of her decision to resign. – Sapa