Nibali covered the 105km challenge, which finished an altitude sickness inducing 3,275 metres above sea level, in three hours, 19 minutes, and 54 seconds.
"It's tough," Nibali said "Especially the last 10 kilometres, 27% climbing is amazing. Despite winning, this battle has been very hard."
This year, the event attracted 592 mountain goats from around the world including Nibali's team manager Brent Copeland and brother Antonio.
Cadel Evans was along for the ride too and slipped in to the top 10.
Emma Pooley took out the women's category, with fellow Brits Hayley Simmonds and Emily-Grace Collinge joining her on the podium.
Australian pro cyclist Carlee Taylor was just happy to finish.
If you've got the time, watch a replay of the race here: