In his ruling on Thursday afternoon, Judge Dennis Davis said there were gaps in the National Assembly rules, but found it was not for the court to dictate to Parliament.
The application was brought on Tuesday by Democratic Alliance parliamentary leader Lindiwe Mazibuko on behalf of eight opposition parties.
It sought to compel National Assembly speaker Max Sisulu to schedule the motion of no confidence debate before Parliament went into recess.
Opposition parties, including the African Christian Democratic Party, the Azanian People's Organisation, the Congress of the People, the Democratic Alliance, the Freedom Front Plus, the Inkatha Freedom Party, the United Christian Democratic Party and the African People's Convention, tabled the motion in the National Assembly.
The parties said the motion was motivated by the Marikana killings; the Nkandlagate scandal; the failure by the government to deliver textbooks and workbooks to school children in Limpopo and the Eastern Cape; the downgrading of South Africa's credit rating by two major ratings agencies; the mounting disrespect for our Constitution and judiciary; unemployment; and the "uncontrollable and rising tide" of corruption in the public service.
Shortly after Mazibuko tabled the motion, the ANC tabled a counter-motion proposing that Parliament reaffirm its full confidence in Zuma's leadership. In a statement, the ANC said it had reaffirmed its "resolve to quash any frivolous and narrow publicity-seeking gimmicks masquerading as motions in the National Assembly by some opposition parties".
Moloto Mothapo, spokesperson for the party's chief whip, said that the motion was not based on any fact or evidence, and therefore amounts to nothing but character assassination.
But according to legal experts, the ANC soon realised its decision to oppose the motion was unconstitutional and backtracked.
"The ANC can't decide what is debated upon. That's illegal. They can merely decide how to prioritise the matter as they have done now," constitutional law expert Pierre de Vos told the Mail & Guardian.
The motion of no confidence was largely interpreted as a move by opposition parties to sound out MPs who had become disenchanted with Zuma's leadership in the run-up to the ANC elective conference in Mangaung.
As such, opposition parties requested the vote to be held by secret ballot.
Pressure on judiciary
Earlier this week Davis lashed out at the politicians for rushing to courts to decide on the matter, saying it was ridiculous to put so much pressure on judges on something so important.
"Can the courts start saying to Parliament, sorry you have to rearrange your schedule? The case has enormous implications.
"Courts are increasing getting drawn into difficult issues.
"How do I tell the speaker and the chief whip that as a judge, I think your priorities were wrong?" – Sapa