Last down the start ramp, the ITT world champion stopped the clock at four minutes and 22 seconds, seven seconds faster than Van Der Breggen (Boels-Dolmans) with European ITT champion Van Dijk (Sunweb) another second back.
Van Vleuten's Mitchelton-Scott team mate Sarah Roy was the fastest Australian home, finishing ninth with a time of four minutes and 34 seconds.
"When you pass the finish line in a prologue it always hurts like crazy and it never feels like you did a good job," the I tried to go out of the saddle in the last 200metres but I felt like I could almost not pedal anymore. My legs were completely full with lactic acid so I knew that I didn't leave anything out there.
"Then they told me I won by seven seconds, so that was a big surprise. Last year I won the prologue in my home town by five seconds in five kilometres, so now to win in three kilometres with seven seconds is surprising.
"It was super cool to win here in my rainbow jersey, almost in my backyard. It is so cool to show off the rainbow stripes with a win.
"Gene Bates (sport director) told me I didn't take time in the corners but on the straight parts, so that is nice for me to know that I have some power and it gives me confidence for this tour but also going into the world championships.
"All the team did very well, so it is nice to see all the training we have done on the time trial bikes is paying off. We have a lot of confidence now and everybody is in good shape."