Nibali’s main rivals, Chris Froome (Sky) and Alberto Contador (Tinkoff Saxo), finished safely in the lead group, but another of the big four, Nairo Quintana, also found himself with plenty of ground to make up.
Stage 2 was won by Andre Greipel (Lotto Soudal), who took the green jersey and points classification lead as a result, with Fabian Cancellara (Trek Factory Racing) grabbing the yellow leader’s jersey by finishing third on the 166km route.
Nibali, who is 2min 9sec off the lead in the overal classification, was caught in a crash some 50km from the finish line as Etixx-Quick Step pulled the peloton along through crosswinds and rain from the North Sea. The 30-year-old couldn’t make contact with the leaders after that, and his efforts were compounded further by a puncture.
Movistar rider Quintana, 25, was also caught out in a hectic ride, and Nibali summed things up when he admitted he had no idea what was going on.
"We were following all day. I was behind (a crash) and I didn't quite understand what was happening," Nibali said, which proved a common theme among several riders after the finish.
"I managed to stay on my bike but I lost some ground there and to compound matters I also punctured.
"It was a question of bad luck, not my legs. That's cycling. You also have to accept these things."
Quintana’s sentiment was similar.
"With the rain and the crashes we had a bit of bad luck and we lost a bit of time, but we hope to get that back day by day," the Colombian said.
"We managed to maintain the team and worked with Astana to avoid losing more time."
Froome, the 2013 champion, remained in good shape thanks largely to a mammoth effort from Sky team-mates Ian Stannard and Geraint Thomas, who provided protection in amongst the chaos. he also made mention of the uncertainty that swept through the peloton just like the wind and rain.
"It was great to be up there with G (Thomas) and Yogi (Stannard) at the end. They did a great job in keeping me protected," said Froome.
"This is their playground and the classics style of racing is what they were born to do.
"This is a huge advantage for us now. We're two days down and I couldn't have hoped for much more at this point in the race."