The Dutchman had a lonely chase to the finish of the 222km Queen stage from Rovett to Bormio after he was forced to stop with 30km left to relieve intestinal problems.
As he dug deep to limit the damage to his overall chances, Vincenzo Nibali (Bahrain-Merida) and Nairo Quintana (Movistar) did as much as they could to enhance theirs, with Nibali winning the stage and Quintana now in with a chance to snatch the race lead.
“I saved the jersey but if you consider that I chased alone for the last 35km and I only lost two minutes, my legs were very good," Dumoulin said. "I had the legs to follow Quintana and Nibali today. That’s why I’m very disappointed to have lost time today because of a problem I had.
There was controversy surrounding Nibali's and Quintana's actions after Dumoulin's misfortune, with some suggesting one of cycling's "unwritten rules" demanded they should have waited for the race leader to rejoin the peloton.
However, the Sunweb rider saw it differently, saying there was no comparison to him generously waiting for Quintana after the Colombian had crashed on Stage 15.
"When it happened, the race was on, it was full gas and Steven Kruijswijk (LottoNL-Jumbo) was at the front," he said. "It was a different situation to Quintana’s crash on Sunday. I couldn’t expect my rivals to let Kruijswijk at the front."
With his lead now contestable, Dumoulin will have the opportunity to show how good his legs really are with Quintana and Nibali now highly motivated after their successful Stage 16 outing.
"It’s definitely not finished but I have to overcome my anger to look further into the Giro. I’m angry with myself.”