Nys, riding for Lidl-Trek, who won the first stage on an uphill finish on Monday, repeated the trick by winning again on a steep finish, beating Italy's Diego Ulissi of Team UAE to the line after 156.5km between Walbrzych and Duszniki-Zdroj.
Vingegaard took no risks in the tight finish, coming in ninth to remain 19 seconds ahead of Ulissi in the overall standings.
The Dane's Visma-Lease-a-Bike teammate Wilco Kelderman completed the day's podium, finishing in third.