Favourite Prevc was second after the first round, behind Nikaido, but turned the contest on its head in the final, soaring 141.5 metres to finish 6.8 points ahead of the Japanese jumper, drawing wild cheers from the large Slovenian contingent in the Predazzo Stadium in Val di Fiemme.
In wet conditions, ski jumpers were wary of their suits becoming waterlogged, prompting a series of countermeasures as a mix of rain and snow fell at the top of the hill.
"I have this privilege to do really good under pressure," Prevc, who sits top of the World Cup standings, told Reuters.
"I was just enjoying this, remembering why you started to do this and just fly as hard as possible."
For Nikaido, the silver medal left a bitter taste after he won bronze in the normal hill.
"I am a bit disappointed that I could not win the gold medal," he said, adding that he was upset with himself that he could not manage a bigger jump in the final round.
Germany’s Philipp Raimund, who won gold in the men’s normal hill individual competition, finished ninth. Daniel Tschofenig of Austria got only one round of the competition as he was disqualified because his boots were four millimetres too long, with an FIS official saying it had been an oversight.