Government leader Penny Wong said the senator's outburst sought to "incite outrage and grievance".
"This is part of a trend that we do see internationally which, quite frankly, we do not need here in Australia," Senator Wong told parliament on Monday.
Senator Thorpe challenged the King and Queen Camilla during a welcome reception at Parliament House in October.
The Indigenous senator claimed the monarch had "committed genocide against our people" and urged him to "give us what you stole from us - our bones, our skulls, our babies, our people".
Penny Wong said Lidia Thorpe's outburst "sought to incite outrage and grievance". (Mick Tsikas/AAP PHOTOS)
Senator Wong said the censure vote - 46-12 - signalled that Australian politicians should uphold standards of respect during visits by dignitaries.
Senator Thorpe arrived in the chamber after the vote, citing a plane delay for her absence.
"Shame on you all" she said.
"If (the king) comes back in, I'll do it again."
Greens senator Mehreen Faruqi decried the motion and called on politicians to listen to the concerns of Indigenous Australians.
"The bubble of white privilege that encapsulates this parliament is a systemic issue," she said.
"That's why we are here today, debating a Black senator being censured for telling the truth of the British crown's genocide on First Nations people and telling it the way she wants to."
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