Under the motion that passed with a vote of 68-32, Zephyr will be allowed to vote but is barred from the House floor, anteroom or gallery for the remainder of the legislative session, scheduled to end on May 10.
Montana Speaker of the House Matt Regier, told reporters, "For Representative Zephyr, an apology would be a great step."
The discord in Montana - which has garnered national attention amid an escalating culture war in the US over issues like transgender rights - has brewed since an April 18 debate over Senate Bill 99. The state measure seeks to ban transgender healthcare treatments for minors, including puberty blockers and hormones.
Zephyr, a first-term representative from Missoula, said in the debate that denying such care was "tantamount to torture," and that a ban would lead to more suicides.
"If you vote yes on this bill and yes on these amendments, I hope the next time there's an invocation when you bow your heads in prayer, you see the blood on your hands," Zephyr said.
In response, the Republican supermajority silenced her within the chamber until she apologized, prompting a large protest by Zephyr supporters at the statehouse on Monday.
When protesters in the gallery disrupted that session by chanting "Let her speak!," the House speaker ordered representatives to abandon the floor, but Zephyr stayed in place, pointing a microphone toward her supporters.
Seven demonstrators were arrested, and Republicans increased their attention on Zephyr, with the ultraconservative Montana Freedom Caucus on Monday urging she is punished.
Majority Leader Sue Vinton, who presented the motion, stressed the need for decorum so that the rights of all representatives were protected.
The Democratic Party, the American Civil Liberties Union and LGBTQ advocates criticized the censure as undemocratic.
Republican legislators across the country have sought to ban certain healthcare for transgender youth. One tracker by a group of independent journalists says more than 500 bills have been introduced that they say would infringe on the rights of gender non-conforming people.
Such bills were once mostly limited to regulating changing rooms and women's sports but now also include limiting healthcare access for transgender adults and in some cases seek to charge parents and doctors with child abuse if they provide treatment.
Opponents of such treatment are sceptical of the major medical associations that support gender-affirming care, raising concerns that minors are too easily allowed to make such life-changing decisions.
Reuters