The Federal Court previously dismissed a challenge launched by Jikilaruwu traditional owner Simon Munkara to the oil and gas company's 262-kilometre Barossa gas export pipeline planned for the Timor Sea.
Santos pursued The Environmental Defenders Office for costs over the dispute, with a court order issued on Thursday showing the parties agreed on a sum of $9,042,093.05.
EDO chief executive David Morris said the firm would pay Santos.
"After careful consultation with our insurer and with deep consideration of the best interests of our clients, staff and the organisation, EDO has agreed to resolve the claim," he said on Thursday.
Northern Territory Environment Minister Joshua Burgoyne said the cost order "calls out environmental lawfare".
"We won't allow activists and economic vandals to manipulate their way into halting or delaying key Territory projects with mistruths and false information," he said.
Santos said the $9 million represented all its legal costs.
It also said the overall Barossa Gas Project and the associated Darwin LNG Life Extension project would create about 600 jobs during the construction phase and about 350 jobs for the next 20 years of gas production.
Mr Munkara had argued the Jikilaruwu, Munupi and Malawu peoples of the Tiwi Islands had a spiritual connection to the area of sea country where the pipeline would pass, and underwater cultural heritage would be at risk by its construction to the west of Bathurst Island.
Tiwi people said the pipeline would disturb the Jirakupai or the Crocodile Man songline, which runs from Cape Fourcroy on the westernmost point of Bathurst Island into the deep sea near the pipeline route.
They were also concerned about the potential impact of the travels of an ancestral being of fundamental importance in their culture, Ampiji, a rainbow serpent.
Justice Natalie Charlesworth granted the emergency interim injunction, stopping work from beginning on the pipeline, just hours before it was due to start in November 2023.
In a further November hearing the judge granted a partial interim injunction to restrain work on the pipeline, except in an area about 75km north of the Tiwi Islands and further.
In her ruling on the case in January, Justice Charlesworth was critical of a geoscientist's evidence who had done a cultural mapping exercise with Tiwi Islanders.
She said an expert report based on the findings lacked integrity in parts and she was not satisfied there was a risk of an environmental impact on the sea country.
The judge said traditional owners' accounts about the Ampiji and the Crocodile Man songlines varied significantly and she was not satisfied the evidence could be characterised as a "cultural feature" of an area, place or ecosystem.
