Huber closed out the stage in a time of 3hr 01min 57sec ahead of Australian Brendan Johnston and the Italian Nicholas Pettina.
After his battle with Johnston the two-time winner said that it was the toughest Crocodile Trophy stage he’d ever ridden.
“My whole body aches, especially my lower back, that was hard work today," Huber said.
Now in fourth place overall, Johnston, who finished just 39sec behind Huber, said that he's playing a patient game while enjoying the terrain.
"Today “was exactly what I love about mountain biking, I’d rather do 100km on this sort of terrain than race on a road or fire trail," Johnston said.
“Urs (Huber) and I race together all day today and with 2km to go he attacked. My plan is to race a smart race, we still have six stages to go and the really long days are still ahead."
The consistent Pettina finished in third with a gap of 2min 39sec to Huber which moved him into second spot overall, ahead of Denmark’s Soren Nissen, who finished fifth on the stage.
In the two-woman elite race Australian White clocked 4hr 06min 24sec to further build her lead on German Regina Genser to 37min 26sec.
“Don’t get me wrong, it was tough and when we were on top of the first climb rain set in, which made some of the rocks really slippery. It took all my skill to stay upright and I’m glad I could keep my lead," White said.
Genser struggled with two crashes, a flat tire and a slipped chain but remained optimistic about the experience.
"I've never ridden so much single track in one go ever. You don’t get that in Europe anywhere, especially not in a marathon," Genser said.
The 80km fourth stage will take the riders from Atherton onto the top of the Great Dividing Range in the Herberton State Forest and will include several climbs totalling 2200m of elevation.