Judge Hamilton Cele dismissed the prosecutor's application on Wednesday, adding no costs were ordered.
"The applicant has not shown the existence of any extraordinary or compelling, urgent circumstances to justify a final declaration of the unlawfulness of her suspension," Cele said in his judgment.
"There are reasonable prospects that if the disciplinary hearing against her is persisted with, it will be finalised within a reasonable time period. If not, she may refer an unfair labour practice."
Cele said the court would intervene in uncompleted disciplinary proceedings only in "exceptional circumstances". He said unfair labour disputes needed to be referred to the Commission for Conciliation, Mediation and Arbitration or to the bargaining council.
"This court [the Labour Court] does not have jurisdiction to adjudicate on a suspension, whether categorised as unlawful or unfair."
But Cele said that if the NPA did exercise its right to discipline Breytenbach, it could be found to be "flouting and frustrating" the aims of an investigation ordered by the North Gauteng High Court into the suspension of former crime intelligence boss Richard Mdluli.
"It has been shown in these proceedings that the applicant will probably be a vital official in that probe," said the judge. "If she is found guilty and dismissed, she will be handicapped from utilising the tools of the trade that she might need in these investigations.
"The justice sought to be striven for in the matter of General Mdluli would have been seriously compromised."
Breytenbach was suspended as regional head of the specialised commercial crime unit on April 30, allegedly for conduct relating to cases allocated to her.
She contended that she believed acting national director of public prosecutions Nomgcobo Jiba suspended her in an attempt to protect Mdluli. Cele said that if the NPA was suspending her for her role in the Mdluli matter, it would probably not admit to this.
NPA spokesperson Mthunzi Mhaga told reporters afterwards that Breytenbach was still regarded as an employee.
"We have a disciplinary hearing – which is pending – that will deal with all issues. The hearing might exonerate her, or find her guilty, but we have to allow that process to unfold," he said.
" … For now, she remains an employee of the NPA. I am not aware of any animosity [between Breytenbach and the NPA]."
He could not say whether the hearing would be open to the media, but said there would be more clarity after Media24's application for access was heard by the court.
The NPA previously said that a ruling by the former chairperson of the hearing, advocate Barry Madolo, to allow the media to attend was "contradictory, patently wrong, unenforceable and irrational". – Sapa