Groups fighting TransCanada Corp.'s pipeline appealed a judge's decision last year upholding regulators' approval for the pipeline to cross the state.
But the high court ruled Wednesday that justices didn't "reach the merits of the case" because the lower court lacked jurisdiction to hear the appeal of the Public Utilities Commission's decision.
Attorneys for appealing groups haven't returned telephone messages requesting comment. TransCanada hasn't responded to an email seeking comment.
The project would move crude oil from Canada across Montana and South Dakota to Nebraska, where it would connect with existing pipelines feeding refineries along the Gulf Coast.
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South Dakota's Supreme Court has dismissed an appeal from opponents of the Keystone XL oil pipeline, saying a lower court lacked jurisdiction to hear their cases.