Van Aert led Kooij through the final corner, just 300 metres before the finish, and the Belgian then still had the speed to hold off Irish rider Sam Bennett for second place.
"I can't ask much more than to get a one-two," Kooij said. "With Wout in front to get us first and second into the last corner I knew it was just then straight to the line and luckily we got it."
Sunday's race could be a forerunner of things to come, with a potential for sprint finishes on each of the first six stages before the general classification contest reaches its finale next weekend.
"We will look at it day-by-day but we know there is quite a lot of responsibility on us as a team to control things and get things together either for the sprints or the GC," Kooij added.
"It's quite a hard task to get that right, we have multiple goals and we will see day-by-day how to get it right."
