The 20-year-old Auckland student from the Pukekohe swimming club was joined on the podium by Ukraine's Kateryna Denysenko in second and America's Jessica Long took the bronze medal.
Neiufi won silver in the event at Rio Paralympics in 2016 and also silver at the world champs in London two years ago.
Neiufi displayed plenty of emotion in her win.
"As soon as I touched the wall, I'm not going to lie - I was a bit confused," she said.
"You just finished racing, everything's going through your head and you don't really notice anything, until I heard my teammates cheering in the crowd and I thought 'maybe I should look at the board'.
"As soon as I looked at the board I just got so emotional."
The fact that she had won gold was had not yet sunk in she said, but she knew it was an important victory,
"To represent not only myself but my family, my community, and everyone that has helped me along the way, so I am so grateful for that."
Neiufi will compete again in the S8 50m freestyle on Wednesday at the Tokyo Aquatics Centre.