Van Dijk used her time trialling skills to take a jump on the field and finish ahead of Kirsten Wild (Hitec Products) and Lauretta Hanson of the Australia national team.
The overall race lead changed hands with Germany’s Trixi Worrack (Canyon-SRAM) leading the Boels-Dolmans pair of Kasper Romy and Van Dijk by 17 and 31 seconds respectively, after she finished fifth on the stage.
Wind was again a decisive factor with an early 13 rider attack on the 112km stage led by Stage 1 winner Wild, Van Dijk and Worrack.
Also in the group were Hanson and countrywoman Gracie Elvin (Orica-AIS), but missing the break were another pair of Australians, race leader Katrin Garfoot (Orica-AIS) and Chloe Hosking (Wiggle-High5).
The gap to the chasers reached almost three minutes but reduced as the wind and desperation from the peloton took effect.
From the brealk Elvin took the first intermediate sprint and Hanson the second as the time gap was cut to less than a minute.
Sensing an opportunity, Elvin mde a long range dash for the finish but was brought back with just four kilometres to go.
Holding a 45 second lead and with 2km to go it was looking like a sprint finish for the break, but Van Dijk had other ideas for the final outcome and powered away for the win.
Kirsten Wild leads the points classification (silver jersey) while Australia’s Hanson claims the white pearl jersey for the best young rider.