Five W&J claimants had sought to strike out the Indigenous Land Use Agreement (ILUA), which they say was obtained at a "sham" meeting, however Justice John Reeves dismissed their claims in the federal court in Brisbane on Friday.
Adrian Burragubba, one of the W&J claimants, says the decision was not unexpected.
"We guessed that we were probably going to be ruled against today, so we were prepared for that," he told reporters outside court.
"It's been a long, hard battle for us... this has come at a great pain to us as well as the other members of the Wangan and Jagalingou.
"All Adani has achieved is to separate a people and to destroy the will of the people and not allow us to have free, prior and informed consent."
The decision opens the door for the Queensland government to permanently extinguish W&J native title over sections of land to make way for the mining development.
"We're still asking the state government not to compulsorily acquire our land... while there remains a legal question ahead of us," Mr Burragubba said.
The mining conglomerate authorised the ILUA at a meeting in April 2016, where Adani say the W&J people voted 294-to-one in favour of signing the agreement, which promised jobs and economic benefits for Traditional Owners in exchange for the extinguishment of native title.
It was originally endorsed by seven out of 12 W&J native title claimants, but one claimant, Craig Dallen, has since withdrawn his support, leaving the group split down the middle.
Those opposed to the mine alleged that Adani did not make "reasonable efforts" to identify and include all potential native title holders in the 2016 meeting, and questioned whether attendees were in fact W&J people.
They also claimed Adani failed to properly identify the sections of land where native title would be extinguished, as required by law.
An Adani spokesperson welcomed the decision.
"Following today’s decision we look forward to working with the State Government and the Traditional Owners to take the next steps in order to finalise land tenure for our project," the spokesperson said.
“We will work with the W&J People under the guidance of the ILUA, while respecting the rights, history, future intentions and requests of the Traditional Owners.”
Along with royalties, Adani says the Carmichael mine project will deliver business, education and employment opportunities to the four Traditional Owner groups within the development area, including a 7.5 per cent Indigenous employment target.