Van Vleuten secured third after she finished 24 seconds behind winner Ellen van Dijk and 14 seconds behind Marlen Reusser of Switzerland on the flat 30.3 kilometre course between Knokke-Heist and Bruges.
The Dutch star revealed before the race that the lack of climbing on the World Championship route would make it difficult for her to win with the course playing into the talents of powerhouses such as van Dijk and Reusser.
Despite the result, van Vleuten was not disappointed with her performance and praised the ride of winner van Dijk.
“I expected this outcome but did hope to get the jersey again. I rode a good time trial and never lost power. It went really smoothly. On a course like this that leads to third place,” van Vleuten said.
“I've never averaged power numbers as high as today so I have to be satisfied with my performance and accept that two riders are better on a course like this.
“It's nice for Ellen (van Dijk) to win and finally find a course like this. It was something for the powerhouses. She deserves the win.”
It was a different story for Swiss star Reusser who was unable to hide her disappointment with a second-place finish in a race she said she had built her season around.
It was also really a big dream of mine to win today," Reusser said
“As you say it's my 30th birthday. Actually, it was the biggest goal of the season, so I have to say that I'm really disappointed.
"It's really bitter for me, but to see Ellen won and that she's so happy it makes it a little bit better. I'm disappointed."
Reusser has not given up on World Championship success and is already thinking about her chances at the 2022 UCI Road World Championships in Wollongong.
"For sure I expect to get even better next year," she said.
"I still have the goal to win the World Championships individual time trial. I hope that I can do that next year."