Thembisile Majola served just 20 months of her three-year contract as the director-general of the State Security Agency (SSA).
Before taking over in March 2022, the agency had been without a permanent head since Arthur Fraser's departure in 2018.
Announcing Majol's appointment last year, President Cyril Ramaphosa said it was "an important part of government's work to stabilise the country's intelligence services".
In a statement announcing Majola's resignation on Wednesday, the parties had separated "by mutual consent with the president", effective from 30 November 2023.
"The president has expressed his appreciation to ambassador Majola for her contribution to the reform and rebuilding of the State Security Agency. President Ramaphosa wishes ambassador Majola well in all her future endeavours," the statement said.
When announcing Majola's appointment, Ramaphosa said: "Her appointment is expected to give greater impetus to the implementation of the report of the SSA high-level review panel and the recommendations of the expert panel into the July 2021 unrest."
The panel found that: "The police failed to stop the rioting and looting in July 2021. The reasons for this failure are complex and sometimes not of their making. In some instances, they did not get any intelligence upon which to plan operations."
In September, News24 reported that, more than two years after violent unrest swept through KwaZulu-Natal and Gauteng in the aftermath of former president Jacob Zuma's incarceration for contempt of court, the Hawks had not secured a single conviction.
Majola resigned as deputy minister of energy in 2018 citing family reasons. Before serving in the executive, she held ambassadorships in Senegal, Mauritania, Cape Verde, Gambia and Guinea Bissau.
Following her appointment to the SSA, News24 reported that government insiders said Majola had long been on Ramaphosa's radar due to the respect she commanded in security circles as a result of her history serving the African National Congress in exile.
Her resignation is a blow to an institution that has been in disarray since Zuma's presidency.
Last year, News24 reported that organised criminal networks captured and paralysed the SSA by setting up parallel intelligence structures within the agency and looting upwards of R1.5-billion between 2008 and 2018 to serve Zuma's political interests.
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