Vos finished ahead of Lizzie Deignan (Trek-Segafredo) and two-time stage winner Sarah Roy (Mitchelton-SCOTT) to the line in a bunch sprint after a 62.5km kermesse.
Bonus seconds for the win gave Vos the lead over Deignan by nine seconds. Amy Pieters (Boels Dolmans), second on Stage 1, is third overall.
“I was quite surprised at the gap across the line," Vos said. "I saw an opening at 200 metres to go. I came from the back so I thought ‘Okay if I don’t go now, I will be late’.
"I knew the legs were going to burn so I just kept going. I saw no wheels coming so that was, of course, a great feeling."
Only Canyon-SRAM's Elena Cecchini able to break away from the peloton during the stage held in and around Cyclopark Gravesend. The Italian, who eventually finished fourth on the stage, engaged in a three-lap solo breakaway around the 2.5km circuit before being caught by the peloton.
Deignan now holds the Best British Rider jersey while defending champion Coryn Rivera (Sunweb) keeps the lead in the Eisberg sprints jersey.
Christine Majerus (Boels Dolmans) continues to lead the mountains classification before the serious climbs to come on Stage 3.
