The Swiss rider finished ahead of Soren Nissen from Denmark and Australian Brendan Johnston - with those three riders now also in the first three posotions overall.
Italian Nicholas Pettina dropped out podium position after a flat tyre saw him lose touch with the leaders on the stage.
Australia's Sarah White had a trouble free day and continues as the sole woman in the elite ranks.
The heat delivered everything the riders had expected from Outback racing with the event adding an additional feedzone 12km before the finish to assist riders struggling in the oppressive conditions.
Huber was again able to break-away from the lead group towards the end of the stage to finish in a time of 4hr 7min 20sec, extending his overall lead to 16min 26sec.
Australia’s Johnston said the stage had been the toughest day on a mountain bike in his career.
“I raced 115km as hard as I could go and in 35 degree heat," Johnston said. "The positive was that I finished third on the stage and I moved into third overall with three stages to go.”
He now has a gap of just over half an hour to Huber, but behind him lurks Pettina who is less than four minutes outside of a podium position.
After two hot and dusty days, Stage 7 will take the Crocodile Trophy 127km north to the Skybury Coffee Plantation and closer to the coast.