Federal Court Justice Mordecai Bromberg has ruled the National Offshore Petroleum Safety and Environmental Management Authority should not have approved Santos's drilling off the Tiwi Islands.
Dennis Tipakalippa, who launched the legal action against the regulator's decision, said Wednesday's judgment made him the happiest man alive.
"The most important thing for us is to protect our sea-country," he told AAP in a statement.
"We want Santos and all mining companies to remember - we are powerful, we will fight for our land and sea-country, for our future generations no matter how hard and how long."
The Munupi elder said he was not consulted over the company's environmental plan and feared the project could damage his people's sea-country.
His special counsel Alina Leikin said the judgment would have national and global implications for consultation with First Nations peoples on mining projects.
"It sets a new standard about the depth of consultation that companies are required to conduct with traditional owners before they gain approval for drilling in sea-country," she said in a statement.
Santos, Australia's second-largest independent gas producer, had told the Federal Court it had all necessary approvals to drill eight wells in the Barossa gas field following consultation with stakeholders.
But in his judgment, Justice Bromberg said the regulator should not have been lawfully satisfied the project's drilling plan met the legal criteria.
"The task that NOPSEMA was required to perform could not have been performed in accordance with the regulations on the information provided by Santos," the judge said.
"Furthermore, there was material ... that NOPSEMA was bound to consider which NOPSEMA did not consider."
He ordered the regulator's approval be set aside and the current drilling injunction continue to October 6.
Santos will suspend drilling activities as it awaits either a favourable appeal outcome or the approval of a fresh environment plan, a company spokesperson said.
"Santos will be seeking to expedite these processes," the company told AAP in a statement.
"Given the significance of this decision to us, our international joint venture partners and customers, and the industry more broadly, we consider that it should be reviewed by the full Federal Court on appeal."
Santos was committed to improving its consultation processes and the company's relationship with traditional owners was very important, the spokesperson said.
The offshore gas regulator said it would consider implications of the decision.
During last month's week-long hearing, the court sat at Melville Island where Justice Bromberg heard from several witnesses in words, song and dance.
The court was told how the Munupi people they feared the Santos project would damage the environment and impact their way of life and spiritual wellbeing.
Santos argued the traditional owners from the Tiwi Islands were not relevant stakeholders in the Barossa project so they would not need to be consulted.
The Nurrdalinji Native Title Aboriginal Corporation says it will closely examine the judgment to see what it means for companies hoping to frack for gas in the Beetaloo Basin.
"The Tiwi people's story is our story too," the corporation's chair Johnny Wilson said in a statement.
"We have not been properly consulted by fracking companies, or the Northern Land Council, and when they do consult they often don't consult widely."
The $US3.6 billion ($A5.2b) Barossa project was expected to create up to 600 jobs and pipe gas 280km to the Darwin LNG facility, with first production originally expected in 2025.
The company said the project, which it purchased from ConocoPhillips in 2020, was 43 per cent complete and on schedule.
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