With an 11th-hour attempt to stop e-tolling by the FF Plus also dismissed, Gauteng motorists will to have to face paying for the use of highways.
An application by the Freedom Front Plus to stop e-tolling on Gauteng's highways was struck from the roll by the high court in Pretoria on Monday.
"The matter is scrapped from the roll for the lack of urgency," said Judge Maria Jansen.
She said the applicant sought wide-reaching relief, and failed to make a proper case.
The e-toll gantries are now expected to go live at midnight on Monday.
Meanwhile, church leaders also vowed on Monday they would not pay toll fees, and called on others to do the same.
"We ... church leaders have therefore decided to publicly declare our intention to refuse to buy e-tags and to refuse to pay this unjust e-toll," they said in a statement.
"We call on all other church leaders, members of our churches and all South Africans who support democracy to do the same."
The leaders, including South African Council of Churches president Bishop Jo Seoka, Central Methodist Mission Bishop Paul Verryn, and Methodist Church of Southern Africa presiding Bishop Zipho Siwa, said the decision had not been easy but had to be made, as the government was not listening to the people.
Also on Monday, lawyers representing the South African National Roads Agency Limited (Sanral) threatened legal action, following a request for clarification on e-toll prosecutions, said the Justice Project SA (JPSA).
On Friday, the JPSA said it had sent a letter to Sanral chief executive Nazir Alli, Transport Minister Dipuo Peters, Justice Minister Jeff Radebe, and national director of public prosecutions Mxolisi Nxasana.
In it, the JPSA asked for details of the exact legal and administrative processes to be followed for the collection of e-tolls and against those who did not pay.
If this was not forthcoming by noon on Friday, JPSA said its attorneys would approach the high court for clarity.
A response was sent by Werksmans Attorneys, acting on behalf of Sanral, said JPSA chairperson Howard Dembovsky.
It was told Sanral was not in a position to clarify matters reported by members of the media, where such clarity should be sought from the reporters concerned.
All the information the JPSA sought was contained in the various government gazettes about e-tolls, and should an application be brought to the courts, Sanral would seek a costs award against JPSA, with "such an application ... an outright abuse of process", the response said.
Sanral was not immediately available to comment.
On Sunday, Peters said more than 750 000 motorists had registered and bought e-tags.
"It's in your best interests that you get tagged.
"This will enable you to gain access to discounts offered to tag holders by Sanral.
"We are aware of campaigns discouraging people from registering, and we wish to encourage motorists to not pay attention to such," Peters said.
However, on Monday the Opposition to Urban Tolling Alliance (Outa) continued to urge motorists to refrain from buying e-tags.
"There is no law that requires road users to buy an e-tag or register with Sanral in order to use Gauteng's freeways," said Outa chairperson Wayne Duvenage.
He said registering would merely make enforcing e-tolling easier, as motorists would be placed on the Sanral system and be bound to a contract to pay for using the tolled freeways.
"Getting e-tagged also limits the right of road users to object to paying tolls and to resist an unjust system."
In October, Outa lost an appeal against a high court ruling rejecting an application to have the implementation of e-tolls set aside.
On November 20, Peters announced that e-tolling would begin on December 3.
Sanral later warned that a hefty bill awaited unregistered motorists without e-toll accounts who failed to pay for e-tolls within a week.
On Friday, the marketing research company Ipsos said in an e-toll survey conducted from October 11 to November 21, four in 10 Gauteng motorists indicated they might buy e-tags, or already had.
According to the study, only one in 10 drivers in Gauteng (10%) strongly agreed with the statement "I have bought an e-toll tag already or intend to buy one", Ipsos said.
E-tolls have dominated headlines several times this year, with most media houses covering the opposition to the new electronic tolling system, according to Media Tenor South Africa.
Analysis conducted by the media research company showed that stories on e-tolls made up 40% of coverage on transport-related issues in Gauteng.
The result of the analysis was based on 3 304 statements on e-tolls in the print media and on television news programmes from January 1 to October 30 this year.
"As the media continues to focus on the political fallout of e-tolls, this could affect the ANC Gauteng support base in next year's elections and further blur the dividing line between government and the ANC," said Media Tenor South Africa researcher Ludene Brown. – Sapa