The Dutchman stopped with 35 kilometres to race, lifted the leader's pink jersey over his head and pulled down his black Sunweb shorts to relieve himself in the flanking green grass.
>>> ‘The race was on, we couldn’t wait for him’ say Tom Dumoulin’s Giro d’Italia rivals
The group continued without him over the Stelvio to Bormio, back into Italy from Switzerland, and took his lead from 2-41 minutes to 31 seconds.
"I had the same problem in the Tour de France last year and then I won the queen stage to Andorra," the Dutchman said after stepping off the podium.
"I hope to recover. I hope I'm not sick and it's the same problem as last year. That'd mean the Giro is not over."
Dumoulin ploughed ahead to maintain his gap to the leaders at one minute, but slid behind when eventual stage winner Vincenzo Nibali (Bahrain-Merida), Nairo Quintana (Movistar), Domenico Pozzovivo (Ag2r La Mondiale) and Ilnur Zakarin (Katusha-Alpecin) began attacking.
"I felt sick all of a sudden, after the top of the Stelvio [78.5 kilometres to race], when we hit the downhill, that's when the problem occurred," Dumoulin added.
"The cause? I don't know, it could be the combination of the altitude and eating more gels than normal because you can't eat bars on a climb like this."
His only team-mate Laurens Ten Dam, who had been in the escape earlier, waited and paced him as far as possible.
"I hadn't seen him since the Mortirolo and then when I came back into the group, it was not a normal Tom that I saw," Ten Dam said. "I said, 'what is going on?' He said, 'hey I need to s**t, I have some problems in my stomach.'
"We had to find the right moment to stop and get rid of the stuff. Once he got rid of it, he found his legs because he was in my wheel yelling, 'Go faster, faster, faster'," Ten Dam continued.
"I was really tired from jumping on the Mortirolo and fighting on the Stelvio so I couldn't help him as much as I wanted."
Dumoulin appeared unusually tired and drained in Bormio when he spoke with the press.
He can now recover before the race continues with its 17th stage to Canazei. In his favour, the stage ends with a gradual summit finish to 1,442 metres. However, he faces several 2000-metre-plus climbs on Thursday in the Dolomites.
"It's really, really disappointing. It was really not necessary," he added. "I only lost two minutes in 33 kilometres chasing alone all the time, so I definitely had the legs to follow Quintana and Nibali."
He said that he should not pay from his solo chase effort to keep Quintana close.
"I think everyone was full-gas from that moment on, I wasn't more full-gas than Nibali or Quintana was. I have to fight all the way to Milan. Do I have another option?!"
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