The 3.95km up-and-down course in La Chaux-de-Fonds included a tricky descent, some serious ramps and unmerciful weather.
The 27-year-old Basque all rounder won the stage with a sensational descent following his second quickest time through the intermediate point at the Côte de la Route de la Montagne. He was only beaten at this point by Belgian youngster Louis Vervaeke (Lotto Soudal) who eventually finished in eigth, 11 seconds behind Izagirre.
Tom Dumoulin (Giant-Alpecin) was the nearest contender six seconds shy of the win, with Michael Kwiatkowski (Sky) rounding off the podium at seconds.
"I knew my condition was still great after the classics and this result is a happy confirmation of that,” said Izagirre.
“We checked the course at noon today and I really liked it, with that short, sharp climb followed by the technical descent, through the small houses before the finish. It all turned out well and we're so happy to get this win,” he said.
Ion Izagirre’s brother and team-mate, Gorka Izagirre, finished in fifth place, eight seconds off the win. Gorka’s actions proved critical in assisting Ion with last minute decisions before taking to the start ramp himself.
“I was doubtful about which bike should I bring into this course, the road race one or the TT one,” said Ion Izagirre.
“I saw Gorka doing great on the Speedmax and I took a last-minute change, when I was already set to start with the traditional one. To be honest, my brother played a big part in this victory, with those good time checks, he was fantastic.
“Now it's time to enjoy this victory. We don't know how the week will go. We've got a strong team, with Nairo (Quintana) always on good form, Andrey (Amador) testing his legs before the Giro...Let's hope we can keep this jersey!"
Quintana was fourth over the intermediate time point and still managed to claim the 18th place despite going as safe as he could through the wet downhill. He sits 16 seconds behind his victorious team-mate, with his race strategy landing him ahead of other general classification rivals.
As bad weather rolled in during the day, and the window for clear weather closed in the face of snow, riders' start times had a big impact on their results.
Chris Froome (Sky), who finished in 60th, didn't hold back on Twitter and suggested the stage should have been cancelled. Froome cited a possible conflict of interest as David Chassot, the delegate and rider representative for extreme weather conditions, is the brother of race organiser, Richard Chassot.
Tonight’s stage is a 167km trek towards Moudon. There are three categorized climbs on the route and almost no respite for the general classification riders, who will be hoping the weather improves as the roads hit the mountains.