Home Affairs Minister Tony Burke refused the far-right firebrand's visa in October 2024 on the basis her visit was not in the national interest and that she would "incite discord" in the community during a planned national speaking tour.
Ms Owens argued her visa rejection went against implied freedom of political communication and that the minister incorrectly interpreted the law.
But the High Court unanimously ruled on Wednesday the visa refusal valid.
In a lengthy published judgement, the court said the law applied where the visa applicant would "stir up strife or dissension in the Australian community" that would lead to harm or danger.
"In the absence of evidence, or agreed facts, it is not obvious that the opportunity to hear Ms Farmer speak in Australia (the so-called 'lightning bolt' effect) could add anything to political communication in Australia," it said, using her married name.
The judgment stated the minister found the evidence was clear that using online platforms for this type of rhetoric can lead to "increased hate crimes, radicalisation of individuals and heightened tensions in communities".
Mr Burke blocked Ms Owens' visa application on the ground he "reasonably suspected" she did not pass the character test.
He decided there was a risk she would "incite discord in the Australian community" and that allowing her into the country would be against the national interest due to her "controversial and conspiratorial views".
Ms Owens' lawyers argued the character test on which visa decisions are made was more likely to exclude non-mainstream political views by saying they sparked division.
Perry Herzfeld SC contended the threshold of "inciting discord" to reject a visa on character grounds was so broad it could capture disagreements and robust debates and was "very much in the eye of the beholder".
This meant visas could be withheld from people who "will stimulate debate ... the minister doesn't like", he argued in the High Court in May.
However, the High Court held the visa refusal was justified and did not infringe on the implied freedom of political communication.
Ms Owens was ordered to pay the costs of the appeal.
When refusing the visa, Mr Burke took into account Ms Owens' inflammatory comments views on Muslim, Black, Jewish and LGBTQI communities which generated "controversy and hatred".
Court documents pointed to her being named in the manifesto of the man who claimed responsibility for a massacre at two New Zealand mosques.
Ms Owens has an influence of over 18 million followers on across her social media platforms, including X, YouTube and Instagram.
