"The application was dismissed," Breytenbach said after proceedings on Friday. She declined to comment further.
Earlier in July, Judge Hilary Rabkin-Naicker heard arguments from lawyers representing the National Prosecuting Authority (NPA) and Breytenbach.
Andrew Redding SC, for Breytenbach, submitted that her new job was not the same as the one she had before her suspension in April 2012 for a disciplinary hearing on 15 charges, all of which were dismissed in May.
The charges included failing to act impartially while investigating the Kumba/Iron Ore/Sishen and Imperial Crown Trading (ICT) mining rights issue.
"The position to which she has been transferred is in no way the equivalent of the position she used to hold," said Redding.
Redding described the NPA's conduct since Breytenbach's suspension as unusual.
"What began as an investigation into her conduct blew up into … a federal case against her," he told the court.
Redding contended that the prosecuting authority had done all it could to prevent her returning to her position from the day on which the NPA levelled allegations against her.
Redding claimed the NPA still considered Breytenbach as suspended. He said this was based on letters between her lawyer and the NPA after she was cleared, at a disciplinary hearing, of all 15 charges against her on May 27.
The following day, the NPA announced it would bring a court challenge against the ruling because it considered the findings "factually incorrect and legally unsustainable".
"Investigating more charges against me smacks of a witchhunt, where [the NPA] appears willing to do anything to prevent me from going back to my post and prosecutions I was handling," Breytenbach reportedly said in an affidavit in June.
The NPA wanted to place Breytenbach on special leave pending a review of the disciplinary hearing's findings. At a meeting held on Breytenbach's return to work, she was told there were allegations of misconduct against her.
"[The NPA] … is doing all it can do to prevent Ms Breytenbach from getting her hands on the docket of … [former police crime intelligence head Richard] Mdluli," Redding said.
Breytenbach brought an urgent application to get her job back as regional head of the NPA's specialised commercial crime unit in Pretoria.
Crime probe stalled
Since Breytenbach was first suspended, she has maintained that the NPA's acting head, advocate Nomgcobo Jiba, and Breytenbach's immediate boss, advocate Lawrence Mrwebi, have gone to extreme lengths to ensure she cannot go after suspended crime intelligence boss Richard Mdluli.
Prior to her suspension, Breytenbach was pursuing the fraud and corruption case against Mdluli.