Traditional custodian Raelene Cooper, a Mardudhunera woman, filed for a judicial review in August of the regulator's decision to approve Woodside's blasting plan.
The challenge argued the National Offshore Petroleum Safety and Environmental Management Authority (NOPSEMA) made a legal error.
Federal Court Justice Craig Colvin agreed.
Despite finding Woodside's legally required consultation with First Nations stakeholders was inadequate, NOPSEMA gave approval for the seismic blasting on July 31 on the condition that further consultation be carried out before blasting began.
Justice Colvin on Thursday set aside the regulator's decision, finding NOPSEMA had erred because the consultation should have been carried out before the approval was granted.
Ms Cooper said she was elated by the decision.
"This is bigger than me, it's about my people and our history," she said.
"I want the old people to remember we are warriors, I'm a warrior and my family are warriors."
Woodside's project is offshore of the Burrup peninsula in northwest WA, known as Murujuga, which is nominated for UNESCO World Heritage listing as it contains the world's largest collection of Aboriginal rock art.
Ms Cooper said the company hadn't properly heard from traditional custodians about the full impacts of their Burrup Hub operations on culture and sacred songlines.
"No one is more relevant to consult about the threat posed by Woodside's Burrup Hub than traditional custodians of Murujuga with cultural, spiritual and family connections to our sacred ngurra (land)," she said.
"We know what it takes to protect our country and keep it safe for all of us - plants, animals and humans.
"When you're messing with Mother Earth you're talking about all humanity, our very existence."
Woodside said it would continue to work with NOPSEMA and all relevant stakeholders to have an accepted environmental plan in place before commencing the seismic survey.
"The decision did not in any way criticise any action by Woodside," a spokesperson said.
"We have consulted extensively on our environment plans, dedicating time and effort so our approach to environmental management and environmental plan consultation meets our current understanding of regulatory requirements and standards."
Justice Colvin had earlier in September granted an urgent interlocutory injunction forcing Woodside to delay the commencement of blasting.
Ms Cooper returned to the Federal Court in Perth on Tuesday for an expedited hearing on the first ground of her case – that NOPSEMA had made a legal error in accepting Woodside's plan when it was not satisfied it had met stakeholder consultation requirements - as well as an issue of legal standing which the court also found in her favour.
Seismic testing involves ships towing special airguns that blast compressed air, creating pulses of sound.
This sound energy is directed at the sea floor and penetrates underlying rock layers, with the sound patterns recorded used to build a picture of geological layers, and oil and gas reserves, beneath the seabed.
According to the Environmental Defender's Office, which represented Ms Cooper, the impacts of seismic blasting on marine animals such as whales can include damage to their hearing and their ability to communicate, stress, displacement from habitat, physical injuries and death.
Woodside argued the ongoing delay to starting its seismic survey is causing significant costs.
The massive Scarborough field is located about 375km off WA's northwest coast.
The gas project will be connected to new offshore facilities by a 430km pipeline to the onshore Pluto liquid natural gas facility, near Karratha.
The project's development phase will include the installation of a floating production unit with eight wells drilled initially, and 13 wells across the life of the gas field.
Woodside expects to process about five to eight million tonnes of gas a year.
The judge awarded costs to Ms Cooper.
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