The Sunweb rider was 49 seconds clear of Team Sky’s Geraint Thomas. Quick-Step Floors’ Bob Jungels followed seven seconds later.
Thomas’ time was originally the time to beat but a strong performance from Dumoulin nullified the British rider’s efforts.
“If I go home now, it’s already been a pretty successful Giro as we’ve got a win and the pink jersey, so it’s a happy day,” said Dumoulin.
“I expected to take time for sure but this much… You never know.
“It depends on the day and today I had a good day. It didn’t feel like it but I fought all the way to the finish.
“Time trials always hurts but it was worth it, the gap was big.”
He will start tomorrow’s stage in the pink jersey as his time has place him first in the general classification.
Top ten results
|1.||Tom Dumoulin - Team Sunweb||50:37|
|2.||Geraint Thomas - Team Sky||51:26|
|3.||Bob Jungels - Quick-Step Floors||51:33|
|4.||Luis León Sanchez - Astana Pro Team||52:17|
|5.||Vasil Kiryienka - Team Sky||52:37|
|6.||Vincenzo Nibali - Bahrain-Merida||52:44|
|7.||Maxime Monfort - Lotto Soudal||52:50|
|8.||Jan Tratnik - CCC Sprandi Polkowice||52:50|
|9.||Jos Van Emden - Team LottoNl-Jumbo||52:52|
|10.||Andrey Amador - Movistar Team||52:53|
|1.||Tom Dumoulin - Team Sunweb||42:57:16|
|2.||Nairo Quintana - Movistar Team||+2:23|
|3.||Bauke Mollema - Trek-Segafredo||+2:38|
|4.||Thibaut Pinot - FDJ||+2:40|
|5.||Vincenzo Nibali - Bahrain-Merida||+2:47|
|6.||Bob Jungels - Quick-Step Floors||+3:56|
|7.||Domenico Pozzovivo - AG2R La Mondiale||+4:05|
|8.||Ilnur Zakarin - Katusha-Alpecin||+4:17|
|9.||Andrey Amador - Movistar Team||+4:39|
|10.||Steven Kruijswijk - Team LottoNl-Jumbo||+5:19|