The hosts added their third goal when Daniel Sampaio latched onto Marco Antonio's pass to slot home in stoppage time.
Jumbo Team's Van Aert produced a powerful sprint in the slight uphill finish to win by half a wheel ahead of Cees Bol and Sam Bennett.
The 28-year-old is now 16th in the overall rankings, 16 seconds behind new leader Yates.
"This is my duty to know my team's weaknesses since I don't want to waste my time," the Croat added.
"My full efforts are totally focused on leading the Badminton World Federation and fulfilling my role as IOC member. I would like to thank the badminton and sporting community for their ongoing support and I look forward to leading the BWF as we plan for our safe return to international badminton," he said.
Valter, 22, broke free during the final few kilometers and the peloton was unable to catch him.
The Bundesliga is also going to intensify its efforts to support football development in China.
"It was a fantastic evening. The conditions, crowd, competition - it was all fabulous. Sam is a fabulous competitor, and I feel we bring the best out of each other," Duplantis added.
Strikers Mehdi Ghaedi and Arsalan Motahari pulled two back for Esteghlal FC in the second half.
France's Julian Alaphilippe, who lost the yellow jersey to Yates on Wednesday after being penalized for 20 seconds for taking a bottle inside the final 20km, sprinted late to finish one second ahead of the peloton.
Other clubs are expected to follow.