The transport department, meanwhile, said it would study the ruling.
"We respect the decision. We will study the ruling thoroughly and decide on the next course of action," it said in a statement.
The Democratic Alliance said the ruling opened the door for getting the system scrapped.
"We trust that during the review process all the financial facts...will come to light and we will learn who stood to make money out of this project," the party's transport spokesperson Neil Campbell said in a statement.
Congress of SA Trade Unions general secretary Zwelinzima Vavi tweeted: "There is no replacement to principle and truth - congratulations!!!"
‘Victory for ordinary citizens’
Afrikaner lobby group AfriForum said the judgment was a victory against the exploitation of ordinary citizens.
"If sufficient motorists were to refuse to register in protest against the system, it will add pressure to the legal actions on Sanral to reconsider the cost effectiveness of the e-toll system as a collection mechanism."
Judge Bill Prinsloo granted an urgent interdict, brought by the Opposition to Urban Tolling Alliance (Outa), to stop the launch of the system, so that a full court review could be carried out to decide if it should be scrapped or not.
"I make the following order... the first respondent [SA National Roads Agency] is interdicted and restrained from levying and collecting tolls," he said.
Prinsloo said that while he realised Sanral would suffer huge financial losses, members of the public would also suffer hardship of the controversial project went ahead.