The below-the-knee amputee broke the Paralympic record in her heat and went even better in the final to beat France's Elodie Lorandi by 0.2 seconds with Mortimer third in 1:01.58.
"I'm pretty gutted I didn't do the sub-one minute," she said. "I would have loved to do that here but we'll save that for another day and tonight was just about going out there and beating those two girls. We are friends outside of the pool but we're rivals in it.
"It was just head down and suck it up on the way back. I just really wanted that gold. That's why there were tears at the end.
"It hurt a lot in the last 15m but I wanted it so badly and it showed what you want, you get.
"This race meant a lot to me and [coach] Roly [Crichton]. We've worked for two years on this, the 100 freestyle. We were fifth in Beijing and to come out with a gold here four years later, it's a great feeling."
New Zealand's 14 medals (five gold, five silver and four bronze) left the country 21st on the medal table, an improvement on the 12 won in Beijing but still short of the pre-Games target of 18. There are still nine events involving Kiwis over the final two days of competition.
Auckland's Rebecca Dubber finished fifth in the S7 400m freestyle final won by Australian Jacqueline Freney in a world record of 4:59.02. It was Freney's seventh gold of the Games.
Cameron Leslie was fifth in the S5 50m backstroke final in an Oceania record time of 42.40 seconds.
Cyclist Fiona Southorn was the best of the Kiwis in the road races, finishing 10th in the C4/5 event. Chris Ross was 18th in the men's C4/5 road race and Nathan Smith didn't finish the C1-3 race.
The final races of the sailing were abandoned in Weymouth because of a lack of wind, meaning the standings after 10 races were final.
Jan Apel and Tim Dempsey were 10th of 11 crews in the two-person SKUD 18 class and Paul Francis was 13th of 16 starters in the 2.4mR.
"I suffered at this event due to a lack of competitive experience" Francis said. "At the moment it's difficult in New Zealand for the sailors with a disability because there's nobody to really race against. I'm disappointed in the way the event has gone from a result point of view."