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The race was won by Canada's Danielle Dorris in a world-record time of 32.99sec tonight, heading off American Mallory Weggemann in 34.30sec and Italy's Giulia Terzi in 34.32sec.
Howarth came home with a time of 36.92, an improvement on her heat time of 38.46sec earlier in the day.
The Te Awamutu swimmer finished fourth in the 100m breaststroke SB7 final on Wednesday, just 1.63 seconds off the bronze medal.
The 22-year-old became New Zealand's youngest Paralympian in London nine years ago, when aged 13, and won gold and silver in medley and butterfly events at Rio.
She had a highly promising go at cycling before returning to the water for the Tokyo Games.