Huber (SUI) finished ahead of Soren Nissen from Denmark and Australian Brendan Johnston to add a third "Croc" to his 2009 and 2010 victories.
Sarah White from Cairns (AUS) took the win in the elite women’s category on Four Mile Beach in Port Douglas after more than 700km and 17,000m of elevation of racing over nine days.
The final time trial stage started the rider field in reverse order of the general classification onto undulating, historic gold rush mining trails and then down the infamous “Bump Track” into Port Douglas.
Huber set off last and with a healthy time gap didn’t take any risks on the rough descent, winning the stage in 54min 24sec and breaking last year’s record time by almost four minutes.
"I'm really happy about my third victory at the Crocodile Trophy. This race has changed so much since I won it last in 2009 and 2010," Huber said.
“Nowadays you really have to be a complete cyclist to win this event. You must have the skills and strength to do well on all terrain, singletrack, rainforest and bush trails and the wide open Outback roads.
"Of course the conditions in Australia are always a challenge, but exactly what makes this race so unique."
Australia's Johnston was third-fastest on the day, confirming his third place overall in the strongest elite field in the history of the race.
"This was the hardest race I've ever done and certainly the longest stage race," Johnston said.
"I’m still young and it was a fantastic experience to race with such strong racers from all over the world. To race onto the top-three podium, I'm happy with that."
Women's winner White finishing in an overall time of 36hr 56min 30sec over the 9 days.
“I really enjoyed this race, my first stage race. I’d love to race it again and would love to see more women in the field, she said.
"It’s a tough race, yes, but absolutely doable. To win so close to home makes me really proud."
SBS/HD will broadcast a special presentation of the Crocodile Trophy on Sunday 22 November from 4:30pm AEDT.