The reigning champion pulled out of the race before the stage of stage 17 to the Col de la Loze, after dramatically falling out of contention at the end of the second week.
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Bernal, 23, has shared an update on Instagram after leaving the race, saying his body told him “enough,” but has not shared any specifics about what caused the collapse.
The Ineos Grenadiers rider said: “Although it sounds strange, I have enjoyed every kilometre I have done on my bike, no matter how painful it was. I enjoyed it because it is my job and my passion.
“I have taken my body to the limit but there came a point where it told me enough and as a defence mechanism has blocked me.”
Bernal had stayed out of trouble in the opening week of the Tour, sitting second overall after stage 12.
But the cracks began to emerge on the road to Puy Mary the following days, when Bernal slipped back to third, a minute off the race lead.
It was far from race over for the Colombian however, based on previous performances, but on stage 15 Bernal cracked 13km from the summit of the Grand Colombier, under the pace set by Wout van Aert for Jumbo-Visma.
By the finish, Bernal had lost more than seven minutes and was out of contention for the yellow jersey.
After crawling through stage 16 in the gruppetto, Bernal then didn’t take to the start of stage 17.
He added: “The only and best option I have had has been to listen to my body and for my health I had to withdraw from the Tour, even wearing number one.
“This is life, this is cycling. I want to thank all the people who have sent me their good wishes. I love you so much!”