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Hewitson started the final 28km leg on Saturday 6min behind American Jason Rawlings.
Keen to close the gap, Hewitson set a hectic pace that both Rawlings and men's supported leader Englishman Keith Burrows struggled to hold.
Hewitson finished the leg in 2hr 4min to claim second, finishing the event 4min ahead of Rawlings after seven stages and 323km of racing in 31hr 34min.
Burrows ran the day's second-fastest final stage to come home 3min after Hewitson to hold on to his men's supported lead with an overall combined time of 30hr 44min, 50min ahead of Hewitson.
In a close battle in the women's unsupported event in which runners have to carry their clothing, food and sleeping bags, Queensland runner Sarah Foster finished the final stage 6min ahead of Emily Kratz from the United States.
But Kratz held on to her overall lead, winning the event in 37hr 2min, 18min clear of Foster.
With a combined time of 35hr, Australian Katy Anderson won the women's supported event by 1hr 7min from New Zealander Kelly Sutherland, and was an impressive fourth overall. Sutherland was seventh overall.
The men's unsupported race was won by former US Special Operations Ranger Seth Campbell, who now lives in New Zealand. He recorded 35hr 18min.
He was 46min ahead of Australian Tim Franklin.
The race started at Mt Cook with 120 competitors, 98 of whom made it to the finish line.