In a letter to staff‚ Mzimela said her resignation was "not a random move".
"I have given this decision careful thought and feel that now is the best time to relinquish my position as your CEO and allow somebody else to pilot the company into the future‚" she said.
South African Airways (SAA) is expected to report a R1.25-billion loss for the year ended on March 31 when it holds its AGM on October 15.
The exit of Mzimela follows the dramatic walk out by the majority of the board at the airline earlier in October‚ including the chairperson Cheryl Carolus‚ all citing a breakdown in the relationship with the shareholder ministry, the public enterprises department.
Last week the airline won support from national treasury after hard negotiations between treasury and the public enterprises department to support the airline‚ which according to the previous board has a debt-to-equity ratio of -359%.
"I leave with some sadness because I have thoroughly enjoyed being a member of the SAA family for almost three years – and will therefore miss the company and all of you‚" Mzimela said.
"I have a sense of relief because steering this mega national asset is‚ to state the obvious‚ a very demanding and daunting task even under the best of times."
"But as many of you know‚ there has not always been a uniform understanding and appreciation of this mandate from stakeholders‚ which bred a myriad of challenges – as if the operating environment was not daunting enough without this unnecessary discourse and misinformation‚" Mzimela said.
Public enterprises department spokesperson Mayihlome Tshwete said the department had been informed of her departure.
"Yes we have received the resignation. We have accepted the resignation, but it was not with immediate effect," said Tshwete.
"She will remain with us for some weeks until we find a suitable person to act in the interim."
SAA spokesperson Tlali Tlali could not confirm the resignation when contacted for comment. – Sapa, I-Net Bridge