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The country's top court dismissed an application from the Squamish Nation, Tsleil-Waututh Nation, Ts'elxweyeqw Tribes and Coldwater Indian Band on Thursday.
As there is no higher court in Canada, the decision brings an end to the groups' years-long legal challenge.
The First Nations were seeking leave to appeal a February decision by the Federal Court of Appeal that found cabinet's approval of the pipeline project in June 2019 was reasonable under the law.
The court did not release reasons for its decision Thursday, as is custom.
Tsleil-Waututh Chief Leah George-Wilson and Syeta'xtn (Chris Lewis) of the Squamish Nation will be hosting a virtual news conference later Thursday.
In a video news conference in April, Tsleil-Waututh and Squamish leaders said they were challenging the adequacy of Indigenous consultation leading up to the second approval of the project.
George-Wilson said the Appeal Court's decision earlier this year represented a setback for reconciliation.
"If unchallenged, it could change the way consultation and consultation cases happen in Canada, making it less meaningful for protecting our inherent constitutionally protected Aboriginal rights,'' George-Wilson said.
The decision relied on a finding that cabinet's determination of its own consultation process was adequate, and the First Nations argue the decision should have been made at arm's length, she said.
"Cabinet is not an expert in consultation and as owners of the project, they were unable to objectively assess the adequacy of their own consultation,'' George-Wilson said.
The Federal Court of Appeal overturned cabinet's first approval of the pipeline expansion in 2018, citing insufficient consultation with Indigenous people and a failure to take into account the effect on marine animals.
After another round of consultations and a second look at how marine life would be affected, cabinet gave the project a green light.
In March, the Supreme Court of Canada decided not to hear five challenges from environment and Indigenous groups from British Columbia, which included the Tsleil-Waututh and the Squamish First Nations.
Some of those groups challenged a Federal Court of Appeal decision in February not to hear their request to consider whether there had been sufficient consultation.
With files from CBC News
[Top photo: The Supreme Court of Canada has rejected an appeal by B.C. First Nations challenging federal approval of the Trans Mountain pipeline expansion project, the Burnaby portion of which is pictured in June 2019. (Ben Nelms/CBC)]