The Mitchelton-Scott rider led the race over the top of the Col du Portillon after attacking the breakaway. Just the descent remained; he was so close to stage victory, like the pepper spray, everyone could taste it.
Eventual stage winner Julian Alaphilippe (Quick-Step Floors) hotly pursued the Brit, and perhaps the pressure of the descent combined with a dampness on the road forced a tumble.
"One of them things," Yates said after the stage. "I've took more risks on more technical descents before and never had any problems.
"You never know what's coming up on some of these corners and it was a bit damp or something and I just came down."
"When you come so close to winning a stage of the Tour it's pretty devastating."
Yates got back on his bike to ride the handful of remaining kilometres and appeared free from serious physical injury.
"Just bad morale," Yates said, appearing to tear up a little. "The morale's pretty damaged right now, you know, when you come so close to winning a stage of the Tour it's pretty devastating not just for me but for the team.
"We've been working for a while for a few stages and when you come that close it's disappointing."
He vowed to fight again on the next stage, the explosive 65 kilometre Stage 17.
"Short stage. My favourite. Beautiful."
Mitchelton-Scott experienced more rotten luck after Damien Howson withdrew from the race prior to the stage start after fracturing his hand in yesterday's crash.
Earlier in the stage, Alaphilippe's team mate Gilbert was also in the race lead on the descent of the Portet d'Aspet but fanged it too hot into a corner, crashing over a wall and into a ravine. Relief for the audience soon came once the Belgian emerged with a thumbs up to the camera.
Later tests confirmed a fracture of the lateral pole of Gilbert's left patella, but he completed the remaining 50 kilometres. He will not start the next stage.
"First of all, I want to say that I'm happy to be here after that tough moment," Gilbert said. "I landed pretty hard on some stones, and initially didn't want to move, but someone from Mavic came and helped me stand up and crawl back from that ravine.
"This isn't how I wanted to finish my Tour and leaving it like this really hurts."
It was another cruel blow for the team after Tim de Clerq withdrew on Stage 16 with an illness.