The Sunweb team rider started the "Queen" mountain stage of the 100th edition with a lead of 2min 41secs on Colombian climbing specialist and 2014 champion Nairo Quintana (Movistar), and with high hopes of becoming the first Dutchman to win the pink jersey.
But by the end of the 222 km ride from Rovetta to Bormio – won by Italy's Vincenzo Nibali (Bahrain team) – Dumoulin's dream was shattered after seeing his lead over Quintana slashed to 31secs.
There were some suggestions his rivals had shown poor sportsmanship, attacking while he made a desperate toilet stop following the first of two ascensions of the Stelvio climb.
"I don't know, it's difficult to say," said Dumoulin, asked if he was angry.
In professional cycling rivals often wait for each other following unexpected incidents to ensure a fair battle.
On Sunday, Movistar leader Quintana thanked Dumoulin for slowing the pace of the peloton when he crashed so he could catch up.
In contrast, no teams slowed when Dumoulin suffered his mishap, the Dutchman forced to hurriedly throw his bike into the grass and rip off his cycling shorts in desperation as he suffered a bout of diarrhea.
"It was a race situation, we were going full gas and I didn't expect them to stop," added Dumoulin.
In the end, he battled on the second ascension of the Stelvio to crest the summit 2:06 behind Quintana and Nibali, and continued his valiant effort on the sinewy downhill to come over the line 2:17 in arrears after Nibali beat Spanish rival Mikel Landa (Sky) in a two-up sprint to end the hosts' long wait for a stage win on the 100th edition.
With another four mountain stages still to come, time-trial specialist Dumoulin was left despondent.
"I'm still in (the leader's jersey) but not with the lead I had hoped for," a dejected-looking Dumoulin said at the finish.
"I'm disappointed with myself. I lost two minutes not because I had bad legs, just because I had other problems.
"It was terrible. I had to stop because I couldn't hold it anymore.
"I had to fight and fight and fight, and take conclusions after the finish. That’s what I did. I'm very disappointed with today."