The Giant-Alpecin rider was closely followed by LottoNL–Jumbo's Primoz Roglic of Slovenia.
Dumoulin completed the flat 9.8km individual time trial in 11 minutes three seconds. Roglic was given the same time, six seconds ahead of third-placed Costa Rican Andrey Amador of Movistar.
The favourites to battle for the podium positions when the race ends in Turin on May 29, Astana's Vincenzo Nibali, Movistar's Alejandro Valverde and Sky's Mikel Landa, finished 17th, 23rd and 68th respectively.
Swiss Fabian Cancellara, 35, who is taking part in his final Giro, was eighth despite starting the day with an upset stomach.
A flat 190km second stage will also take place in Netherlands as the competitors ride from Arnhem to Nijmegen.
Tour de France favourites Alberto Contador, Nairo Quintana, Chris Froome and Thibaut Pinot are skipping the race as they will be targeting medals at the Rio Olympics in August shortly after the conclusion of the Tour.
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by Tony Jimenez)
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