The laws passed on Wednesday make it easier for people to have their gender accurately documented without undergoing sexual reassignment surgery.
A change of name will also be able to be made at the same time as an alteration of sex in support of trans and gender-diverse people in their transition.
The laws have two pathways to alter the record of sex for a child under 16 - through the Children's Court, or with an application to the register by a parent or guardian when particular criteria are met.
The bill replaces the existing Births, Deaths and Marriages Registration Act and allows greater freedom over chosen gender descriptors, including non-binary recognition.
The LNP opposed the laws, arguing a bill allowing self-declaration was a threat to women's privacy in women-only spaces such as toilets and change rooms and would have a negative impact on women's sports.
"This bill is an attack on women, it is an attack on women's rights and it's an attack on young girls," deputy LNP leader Jarrod Bleijie told parliament.
Opposition MPs also raised concerns about children under the age of 16 who might apply to change the gender on their birth certificate.
Attorney-General Yvette D'Ath said the bill had proper safeguards and "does not allow a young person to just go off and randomly make a decision and get these changes made without any proper oversight".
Health Minister Shannon Fentiman, who introduced the bill last year as attorney-general, said the concerns about women's safety were unfounded.
"Despite repeated claims to the contrary, there is no evidence from any jurisdiction to suggest that women will have fewer rights or be less safe," she told parliament.
The legislation also aims to better recognise modern family structure, with same-sex couples able to register as mother/mother or father/father for the first time.
As it stands, only one person can be registered as a child's mother or father.
The changes have been welcomed by groups representing LGBTQI people and their families.
Equality Australia representative and trans woman Ymania Brown said the laws were a life-changing moment for trans and gender-diverse Queenslanders.
"What most people in Australia take for granted as a simple piece of paper is for trans and gender-diverse people the right to exist and be seen for who we are," she said in a statement.
"Everyone deserves the respect and dignity of being recognised as themselves."
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