The Alpecin-Fenix leader was clearly the strongest in the race along with Alaphilippe, jumping away from the peloton multiple times on the hills that define the race.
They were away again in the final, along with Benoît Cosnefroy, the AG2R La Mondiale rider riding a rich vein of form after the Tour de France.
In the end, Van der Poel lost out by less than half a wheel length as Alaphilippe almost repeated his Liège-Bastogne-Liège blunder by celebrating before he crossed the finish line. After the race, Van der Poel admitted his own mistakes in the sprint finish.
He went to the front of the lead trio with 700 metres to go on the final hill of Schavei but let Cosnefroy jump first 200 metres out as the Frenchman took the inside line of the final turn. Van der Poel was then boxed in the final 100 metres as Alaphilippe came around to edge to the win.
"I made a mistake I normally never make," Van der Poel told Het Nieuwsblad after the finish. "I knew the finish from last year, so I knew what I had to do. When Alaphilippe went past I knew I had waited too long.
"I was half-wheeling between him and Cosnefroy. I just waited far too long to go. I can hit myself on the head.
"I was going to do what Cosnefroy did – sprint against the fence because the others would have to come through the wind."
Van der Poel, who extended his team's Europe Tour lead over Arkéa-Samsic by a further 65 points as Warren Barguil took fifth, acknowledged that more opportunities to win will come before the season's end, but said that he would lose sleep over this result.
"I can't forgive myself for messing this up. The next race is coming soon but I can't think about that right now. I was keen to win here. This is going to make me sleep very badly."
Van der Poel's next race will be Gent-Wevelgem on Sunday, with a return to the Tour of Flanders coming a week later and then a debut at Paris-Roubaix. He'll be a prime favourite for those cobbled Classics, with any top result looking set to secure him and his team a ticket to any WorldTour race – including the Tour de France – next season.
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