Dumoulin, of the Sunweb team, flew over the rolling, 39.8 km course in the Sagrantino wine-growing region to finish in a winning time of 50min 37sec and live up to his name as the 'Butterfly of Maastricht'.
Britain's Geraint Thomas (Sky), still nursing a sore arm from the effects of a crash on stage nine, was second at 49secs, with Luxembourg's former race leader Bob Jungels (Quick Step) in third at 56sec and Italy's defending champion Vincenzo Nibali (Bahrain) sixth, at 2min 07sec.
Movistar climbing specialist Quintana was expected to lose significant time to pre-stage favourite Dumoulin, and kept to the formbook over a rolling route from Foligno to Montefalco whose technical finish prompted a number of riders to crash.
After climbing to victory on the summit finish at Blockhaus on stage nine Sunday, Quintana -- covered from head to toe in pink -- dropped to second overall at 2:23 behind Dumoulin after narrowly avoiding disaster when he had to bunny-hop over a traffic divider.
Dutchman, Bauke Mollema (Trek), failed to finish among the top ten but remains third at 2min 38sec, nine seconds ahead of Frenchman Thibaut Pinot (FDJ).
Although the race for the pink jersey will be decided in the climb-heavy third week of the race, Dumoulin was delighted with a stage win that boosts his chances of maintaining his challenge.
"It's a nice gap to go into the mountains with," said Dumoulin. "But like Nairo Quintana showed on (stage nine to) Blockhaus, he's the better climber, and a lot can happen in the third week.
"But this win is in the pocket. It was already a pretty successful Giro for us, but now we have the stage win and the jersey."
"It's a little worse than I was hoping for ... but we'll find a way to claw back some time," Quintana said at the finish.
"Dumoulin was flying, he's a (time trial) specialist. He could be my biggest rival now."
Nibali would beg to differ, although the Italian -- after being left behind by Quintana in the final kilometres of the climb to Blockhaus -- started in ominous fashion.
He failed to register among the top ten at the two checkpoints, at the 9.8km and 29km marks, before improving on the hillier last two-thirds of the course.
Although finishing 2:07 behind Dumoulin, the 2013 and 2016 champion was 46secs faster than Quintana.
"I think I did a good time trial," said the Italian.
Wednesday's stage is a medium mountain stage over 161 km between Florence to Bagno di Romagna.
1. Tom Dumoulin (NED/SUN) 50min 37sec,
2. Geraint Thomas (GBR/SKY) at 49sec,
3. Bob Jungels (LUX/QST) 56,
4. Luis Leon Sanchez (ESP/AST) 1:40,
5. Vasil Kiryienka (BLR/SKY) 2:00,
6. Vincenzo Nibali (ITA/BAH) 2:07,
7. Maxime Monfort (BEL/LOT) 2:13,
8. Jan Tratnik (CZE/CCC) 2:13,
9. Jos van Emden (NED/LNL) 2:15,
10. Andrey Amador (CRC/MOV) 2:16
19. Thibaut Pinot (FRA/FDJ) 2:42,
20. Steven Kruijswijk (NED/TLJ) 2:43,
23. Nairo Quintana (COL/MOV) 2:53,
38. Mikel Landa (ESP/SKY) 4:02
1. Tom Dumoulin (NED/SUN) 42hr 57min 16sec,
2. Nairo Quintana (COL/MOV) at 2:23,
3. Bauke Mollema (NED/TRE) 2:38,
4. Thibaut Pinot (FRA/FDJ) 2:42,
5. Vincenzo Nibali (ITA/BAH) 2:47,
6. Bob Jungels (LUX/QST) 3:50,
7. Domenico Pozzovivo (ITA/ALM) 4:05,
8. Ilnur Zakarin (RUS/KAT) 4:17,
9. Andrey Amador (CRC/MOV) 4:39,
10. Steven Kruijswijk (NED/LNL) 5:19
11. Geraint Thomas (GBR/SKY) 5:36,
42. Mikel Landa (ESP/SKY) 30:38