Nosiviwe Mapisa-Nqakula is accused of soliciting hefty amounts in bribes from a former military contractor when she was defence minister between 2014 and 2021 before being appointed speaker.
She launched an urgent application last month to avoid arrest which she described as "illegal."
"This court is not a means to declare an arrest which has not taken place unlawful or that it would be unlawful or explain a view thereon," the judge Sulet Potterill said.
"I am therefore not granting this order," the judge added.
According to the judge, granting the order would mean "the flood gates will be open," and every suspect would approach the court "on an urgent basis setting out on speculation that there is a weak case against it and interdict an arrest."
Potterill stressed that Mapisa-Nqakula had access to legal representation in the "pre-arrest" stage and that state authorities had been "lenient" on her "and let two weeks go by" since a raid on her home.
Coming just under two months before national elections, the raid adds to the woes of the ruling African National Congress (ANC), which is struggling in the polls amid accusations of graft and mismanagement.
As the May 29 election approaches, the ANC is at risk of dropping below 50 percent of the vote for the first time since it came to power at the end of apartheid in 1994.
In March, investigators raided the home of Mapisa-Nqakula as part of a corruption probe, with which she had vowed to fully cooperate.
Shortly after, she announced she would take "special leave."
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