The 24-year-old had been entirely under the radar but beat off Jasper Philipsen and needed a photo-finish to get ahead of Quick-Step's French tyro Paul Magnier, with Philipsen third.
Pre-race favourite Wout Van Aert of the Visma team finished in 11th but was unable to produce a sprint to rival the strong finishing Waerenskjold.
Van Aert, who registered the same time as the winner on a day featuring 35kph winds, can try his luck again Sunday at Kuurne-Brussels-Kuurne.
"I'm pinching myself, I came to Belgium for Sunday's race and this one rarely ends in a sprint," said the 6ft 2in (191cm) winner.
The East Flanders classic named after the Belgian newspaper Het Nieuwsblad was won in the past three years by Visma, with last year's champion Jan Tratnik now with Bora getting caught out in a split Saturday.
A seven-rider break made up of minor figures took a lead of over five minutes as the peloton rushed out of Gent towards Ninove along a route scattered with cobbled sections.