The bill, approved in December, makes Scotland the first nation of the United Kingdom to back a self-identification process for changing gender, including removing the need for a medical diagnosis of gender dysphoria and lowering the minimum age to 16 from 18.
Jack said he was invoking Section 35 of the 1998 Scotland Act, which allows the UK government to prohibit a bill becoming law if London deems it has an adverse effect on matters where the national government retains ultimate jurisdiction.
"I have not taken this decision lightly," Jack said in a statement, adding it would "have a significant impact" on equalities matters across Britain.
"I have concluded, therefore, that this is the necessary and correct course of action."
Some women's rights campaigners have argued the changes could pose a threat to the safety of women and girls by making it easier for predatory men to access single-sex spaces such as bathrooms.
Supporters of the bill, however, said the reforms benefit transgender people and pose no threat to women's rights.
Other countries including Ireland, Denmark and Argentina have adopted self-ID laws to make it simpler and less invasive to change gender.
The decision is likely to trigger a bitter legal battle between Edinburgh and London, with the Scottish government previously warning it would contest what it described as any attempt to undermine the democratic will of the Scottish parliament, which has devolved powers in certain areas.
(Reporting by Alistair Smout, additional reporting by Kylie MacLellan; editing by William James)
