The president had "held discussions" with Hajaig, following Cabinet's fortnightly meeting on Wednesday morning, government spokesman Themba Maseko told a media briefing at Parliament.
The deputy minister had "expressed her deep regret to the president for making the statement", he said.
"She subsequently apologised unreservedly and unequivocally for the comments, and agreed to withdraw them unconditionally."
Earlier, Cabinet had "expressed concern about the statement as it was contrary to the stated polices of this government regarding anti-Semitic sentiments", he said.
Maseko said Hajaig's remarks were "something that may have been an error of judgement on her part".
While he could not divulge details of the conversation between Motlanthe and Hajaig, he said it was "safe to say that the president would have reiterated government policy that in fact anti-Semitism equates to racism in this country and we will not support any form of racism".
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