Cologna, who has won the past two Tours, was looking to lay down a marker in the sprint having finished fourth in both the prologue and the pursuit to rank fourth overall.
And that appeared to be more than a possibility as he stormed into the final – however his hopes of a first stage win of this Tour de Ski came crashing down at the death.
The Swiss cross-country skier appeared to clip the flag of a fan on the final climb on home soil and fell to the ground with Krogh making his move at that exact moment.
He couldn’t be caught as he won in a time of 3:21.3minutes with Italian Federico Pellegrino exactly a second behind in second and Canadian Len Valjas 0.6seconds adrift third.
Britain’s Andrew Musgrave didn’t make the final but he did record the best-ever result by a Brit on a Tour de Ski stage by reaching the semi-finals in Switzerland.
Russia’s Maxim Vylegzhanin, who also wasn’t involved in the final, still leads overall just 2.1seconds ahead of Cologna as Krogh hailed an unlikely victory.
“I didn’t expect to win; my goal was to get to the semi-finals. To reach the final was satisfying and it was a big bonus to win,” said Krogh.
“It was a tricky course but I liked the track and of course when you win you can’t say you don’t like it. There was a good atmosphere too and I liked that.”