Kerekere also made referenced to the country's first and only transgender MP, Georgina Beyer.
The Bill means people can amend the sex on a birth certificate on simple process without going through the Family Court, which involved appearing before a judge and disclosing private medical information.
It will also not require people to provide evidence of medical treatment, which can be difficult to access, intrusive, and which the person in question may not want.
Internal Affairs Minister Jan Tinetti said it was a "a proud day in Aotearoa's history".
She paid tribute to the people who submitted in favour of the change who had been "hurt, mocked, belittled and discriminated against".
"A lot of discussion was aimed at trans women. As a cis woman I am proud to stand alongside my sisters.
"Trans misogyny is still misogyny."
Tinetti referred to a time when she was principal at a school and an 8-year-old student, who the "world saw as a boy knew they were a girl".
She worked through the journey with her, and she'd recently contacted the minister to thank her.
"We are changing legislation that is truly a step closer to an inclusive Aotearoa New Zealand.
"Keep proudly being you."
National Party spokeswoman for women Nicola Grigg said few bills had had such a "complicated" passage through the House.
"But this Bill is in a much better state than when it was introduced in 2017."
She said she understood the concerns of those who felt the change could diminish the status of women in society, and set a precedent for replacing sex in policy.
"Those views are genuinely held and we as parliamentarians have an obligation to listen."
She said she was concerned some of those opposing the changes were blocked from organising debates on the topic.
However, Gigg said she believed those fears were unfounded.
"The current law causes unnecessary stress for some people and I don't think it will set a precedent. Laws need to reflect the times we live in.
"All this is doing is modernising the process, it was a dated Act and this shifts it in the right direction."
The self-identification provisions come into force in 18 months' time.
This will give the Government opportunity to consult with the rainbow community and receive submissions and ensure the legislation works to support those it concerns.
Consultation will begin next year on the regulations which will determine who is a suitably qualified third party to support applications for young people; find a way to make sure the sex markers available for the birth certificate include non-binary and cultural options; and determine any additional requirements for anyone seeking to amend their registered sex more than once.