Colombia's Nairo Quintana has become the Giro d'Italia's new leader after winning a ninth stage marred by a crash caused by a police motorbike 15 kilometres from the finish.
The motorcycle was stopped at the side of a narrow road at a point when riders were using the full width, just as the climb of Blockhaus started to kick up.
Fellow Briton Adam Yates remained third, 10 seconds back, with most of the overall favorites.
The pair were left behind as the leaders began the final climb up the Blockhaus and Thomas, who needed a couple of minutes to get back on his bike, appeared to be suffering from a shoulder injury. My shoulder popped out as well.
Quintana, the Colombian who won the 2014 Giro and was twice runner-up in the Tour de France, finished 24 seconds ahead of Thibaut Pinot of France, who edged Tom Dumoulin of the Netherlands in a sprint for second. I'm very happy that I won.
Thomas added: "I had felt good and then I crashed and my race was over". "The whole team was strong and I was strong".
Jungels fell the 12th place in the general classification, while Pinot and Dumoulin were able to stay within half a minute of Quintana.
Britain's Geraint Thomas finished six seconds behind the Quick-Step Floors rider retaining his second place. "That's the most important for now".
Yates finished four minutes and 38 seconds behind and Thomas's ordeal ended 5:07 after stage victor and race leader Nairo Quintana had crossed the line.
Quintana dedicated his victory to 2011 Giro champion Michele Scarponi, who died after a collision with a van while training last month.
Astana's Luis Leon Sanchez was third, 10 seconds further adrift, and the fourth rider of the group Valerio Conti of UAE-Emirates crashed taking a corner.
After a rest day Monday, the Giro resumes Tuesday with a 39.8 (25-mile) individual time trial from Foligno to Montefalco through the Sagrantino winemaking region in Umbria.