Van Aert entered the 268-kilometre race as the favourite in Flanders but soon found himself trailing Alaphilippe after an array of rather unexpected attacks from the French team.
The 27-year-old was able to keep pace with the rainbow jersey on each occasion, up until the climb over Smeysberg with 50 kilometres to go, where neither van Aert nor compatriot Jasper Stuyven could take over.
“I’m only human, too,” a disappointed van Aert said after the finish in Leuven.
“Obviously I wasn’t bad but not good enough. I rode the finale and behind Alaphilippe the differences weren’t massive.
“I didn’t make a fool of myself, but I wasn’t good enough. There’s two reasons we didn’t win: Alaphilippe was much stronger than the others and I wasn’t as good as I hoped I would be.
“I didn’t expect we would be put under pressure that early. It was as if they did a wrong count of the laps.
“Already when we did the first Flandrien loop at 200 kilometres from the finish the race was exploding.”
“On the Smeysberg I wasn’t able to follow,” he added.
“Alaphilippe and [Sonny] Colbrelli were certainly among the guys on whose moves I wanted to react.
“It was probably a sign but then again, the hardest part of the race was over.
“Jasper and I were able to set the situation straight quickly. We were still in a good situation.
“Remco [Evenepoel] was able to keep the group together for a very long time. Jasper and I were the guys who had to try something to finish it off in Leuven. That’s what we tried.”
In the end, a go-ahead from van Aert to Stuyven with 20 kilometres to go left the Belgians with too little time to reel in Alaphilippe or even make the podium - a decision van Aert acknowledged could have been made earlier.
“After the Smeysberg climb I could’ve made that call (for Stuyven to lead) but at that moment the situation was still in our favour,” he added.
“I should’ve indicated earlier (that I wasn’t super). It was always the goal to take turns when there were moves, in order to not be in a defensive position but still with the idea that we were riding for me.
“Just before Alaphilippe made his decisive move on the St Anthony climb I told Jasper to race for it because I thought I wasn’t good enough to finish it off.
“Alaphilippe was simply stronger. It would’ve been a nice consolation prize – certainly for Jasper – to be on the podium. That’s a bummer.”
Stuyven, in his hometown, was able to sprint for second place but ultimately missed out on a medal behind France, the Netherlands and Denmark.