But the Slovenian pulled away with a race-winning attack on the final ascent of the Oude Kwaremont with around 15km to go and cruised along the flat roads to a solo victory.
The chasing pack sprinted for the remaining medal positions with Belgian Wout van Aert missing out on a podium finish.
In the women’s race, Belgian Lotte Kopecky made history as the first cyclist to win three editions of the event.
Riding for Team SD Worx, the 29-year-old claimed victory in thrilling style by winning a four-way sprint finish ahead of France’s Pauline Ferrand-Prevot, Liane Lippert of Germany and Poland’s Katarzyna Niewiadoma-Phinney.
“It was a crazy race with a lot of crashes in the beginning,” said Kopecky. “When it went with the four of us I was pretty confident.”
Italian rider Elisa Longo Borghini was among the favourites with Kopecky and also chasing a third Tour of Flanders title, but had to withdraw after crashing around 95km from the finish.
Around 750,000 spectators gathered on the streets from Bruges to Oudenaarde for the event, which is one of five one-day races in the cycling calendar known as the Monuments.
The others are Milan-San Remo, Paris-Roubaix, the Liege-Bastogne-Liege and Tour of Lombardy.
On 13 April, Pogacar will be taking part on more cobbled tracks for the Paris-Roubaix race – known as ‘hell of the north’ – for the first time, where Van der Poel is again the defending champion.
“Roubaix is a completely different race, but I will accept the challenge and try to do my best,” added Pogacar.