There was a planned withdrawal for the team prior to the start of the stage as Primož Roglič withdrew from the race to begin properly healing from injuries suffered in a crash on Stage 5.
The Slovenian had been instrumental in Vingegaard's quest to seize the yellow jersey after sacrificing his own overall aspirations, helping his teammate consistently attack Tadej Pogačar (UAE Team Emirates) during the ascent of the Col du Galibier in Stage 11.
“In order to let my injuries heal, we have decided that I will not start today," Roglič said in a statement from the team.
"I am proud of my contribution to the current state of affairs and I am confident that the team will achieve its yellow and green ambitions. I want to thank everyone for the support.”
Once the fast-paced stage got going on another day of intense heat, the bad news continued for the Dutch team, Steven Kruijswijk caught up in a crash as news of another protest up the road caused indecision in the peloton with 64 kilometres to go.
The 35-year-old looked in serious pain and didn't move after the crash, making the decision to withdraw from the race shortly after.
Green jersey Wout van Aert, who had dropped back to the bunch after forming the early breakaway said he narrowly avoided being caught up along with Kruijswijk.
“We were told that there was another demonstration,” van Aert said. “I don't know if it was because of that, but suddenly it was chaos in the peloton.
"When Steven fell, I barely managed to dodge the fall. I waited first, but it didn't look good."
Only six kilometres later, disaster struck for the team when race leader Vingegaard came down along with Tiesj Benoot in vision that would have had the entire country of Denmark watching with baited breath.
Fortunately both riders were OK to continue, but Vingegaard and co had to go full gas to make up a minute back to a strung-out peloton before making his way up to the front. The Dane didn't sustain any major injuries from the fall but acknowledged the task of riding into Paris with yellow had been made far more difficult with the losses of Roglič and Kruijswijk.
“It was a bad day for us,” Vingegaard said.
“I myself am fine. Tiesj fell for me and I couldn't avoid him. Unfortunately, these kinds of incidents are part of cycling.
"The fact that Steven and Primoz have dropped out is very disappointing. They are important teammates. We will do our best after the rest day and continue to fight until Paris.”
The Tour de France goes into a rest day, but will resume with Stage 16, an intermediate day in the foothills of the Pyrenees that sees the riders traverse 179 kilometres to the finish in Foix. Watch on the SBS SKODA Tour Tracker from 2020 AEST, with the SBS and SBS On Demand broadcast beginning at 9.30 AEST.