"Our reporter who worked on the piece was led down an unsavoury garden path," said editor Makhudu Sefara.
He said the paper apologised to Ramaphosa for the article.
"It's a pity that even with the best of intentions and efforts, errors will creep in and reporters will be misled. We're all fallible. To err is human.
"The point, though, is to avoid or minimise them and to improve quality-control checks.
While Sefara apologised for the Star's error, he also called out other media reports that erroneously said he had disregarded concerns on the article from Independent Newspapers' deputy political editor Gaye Davis.
"For the record, this was not so," he said.
Sefara said Davis had not been in contact with him directly and her complaints about being ignored were due to a misunderstanding between Davis and the writer of the article.
"She has since apologised to me for this incorrect assumption," he said.
Davis resigned on Monday from Independent Newspapers to "publicly disassociated" herself from the article.
She said she had received confirmation from Ramaphosa on Sunday evening that he was accepting the nomination and had spoken to the writer of the article but was told the paper was standing by the story. – Sapa