The ace climber, set to co-lead Euskaltel's Tour de France team alongside Igor Antón this summer, got a flat tire with less than three kilometres to go on an unusually hilly first stage starting and finishing in Champéry.
Seeing as it was not categorized as a flat stage, the three-kilometre rule didn't apply, meaning Nieve ended up ceding the 58 seconds he lost to the group of favourites.
A 70-something group containing most of the pre-race favourites, including Samuel Sánchez, finished the day almost two minutes down on solo victor David Veilleux.
The Canadian had formed part of the day's main break alongside, among others, Euskaltel's plucky Ricardo García, and the Europcar rider decided to go it alone with a massive 47 kilometres left to ride.
He immediately distanced García and co. and ended up coasting to a sensational opening-day victory that puts him firmly in the overall lead.
García long looked to be hanging on for a podium place, but with less than five clicks to go he was reeled in by the peloton.
- (1, David Veilleux (Europcar), 3:17:35)
- 17, Samuel Sánchez, 1:57
- 19, Gorka Izagirre, s.t.
- 45, Mikel Astarloza, s.t.
- 49, Egoi Martínez, s.t.
- 58, Romain Sicard, s.t.
- 91, Mikel Nieve, 2:55
- 93, Ricardo García, 3:30
- 101, Peio Bilbao, 5:51
Photo: Euskaltel Euskadi