The Swiss marathon specialist finished ahead of Denmark’s Sören Nissen and Stage 1 winner Nicholas Pettina of Italy third.
Australian Brendan Johnston and two-time Crocodile Trophy winner Ondrej Fojtik (CZE) tied at fourth.
"After losing a bit of time yesterday, I knew today I'd get the chance to make up for it," Huber said.
"The Danish and Italian riders kept up with me all day and just before the finish I attacked and was able to stay ahead of Nissen."
After a 12km neutral section through Cairns, the race start and climbing began just before Copperlode Dam, the town’s water reservoir.
Used to training and racing in the European Alps, the Swiss marathon athlete Huber coped easily with the early 1500m of elevation and wet conditions, crossing the finish line in 2hr 28min 13sec, half a minute ahead of Nissen.
Pettina followed approximately five minutes later while Johnston and Fojtik came in at seven minutes.
This result shakes things up in the overall standings with Huber holding a gap of 1min 24sec on Nissen with Pettina third ahead of Johnston and Ondrej Fojtik.
Australian Sarah White, increased her race lead in the women’s elite contest to 23 minutes, winning her second consecutive stage ahead of Germany’s Regina Genser
Stage 3 begins after 18km neutral ride from Lake Tinaroo to the town of Athethon followed by two 27km loops in the Atherton Mountain Bike Park.