Overall, Dumoulin now leads previous leader Nairo Quintana by 2:23 after the Colombian lost a massive 2:53.
Dutchman Bauke Mollema (Trek-Segafredo) moved up to third, 2:38 behind his compatriot, after he leapfrogged Frenchman Thibaut Pinot (FDJ), now fourth and two further seconds back at the end of a bad day in the 10th stage.
Thomas, who lost over five minutes after a crash in the ninth stage, revived his podium finish hopes, sitting in 11th place overall, 5:33 off the pace.
Dumoulin will now have to hold off the expected repeated attacks from pure climbers like Pinot, Quintana and defending champion Vincenzo Nibali in future stages if he is to retain the maglia rosa and win his first grand tour.
In 2015, Dumoulin was leading the Vuelta (Tour of Spain) at the start of the penultimate stage but cracked in the last mountain trek after an onslaught from Fabio Aru's Astana team to end up sixth overall.
Wednesday's 11th stage is a 161-km hilly ride from Florence to Bagno Di Romagna.
(Reporting by Julien Pretot; Editing by Larry King)
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