Despite insisting he has good legs, the pre-Tour favourite struggled on Stage 17, losing more time to Sky's Chris Froome.
Maybe it was the post rest day blues which strikes some riders, or perhaps the diminutive Colombian has not timed his last week fitness as well as he hoped prior to the start of the Tour.
Despite strong support from his seemingly ageless team-mate Alejandro Valverde, Quintana finished 27 seconds behind Froome to remain fourth overall but further away than before.
“It wasn’t a great day for me," he said. "I expected to do better because my feelings were good, but my body did not react well into today’s final climbs.
"I did just as much as I could. Let’s hope I can recover to my best and react well to what’s left in this Tour, just as it happened in previous years when I fared better into the final days of racing.
"I feel well, it’s just a bad day. We must focus on recovering and bouncing back to my real status, the fitness I achieved for other races. Anything can happen until Paris."
Puzzlingly for a rider who has finished second twice at the Tour, Quintana then fell back on his relative youth in an attempt to dampen expectations of a general classification recovery.
"There are many years left for me. I’m 26. Many people ahead of me on the standings is quite more experienced. I’ve got time to keep fighting for it.”
While this may be true, Froome and Australia's Richie Porte are both 31 and the consistent Bauke Mollema is 29, Quintana is now a veteran Tour campaigner, with a Giro d'Italia victory to go with those two Tour podium places.
Quintana is speaking as if he has all the time in the world, but regardless of age, a Tour victory is no inevitability. In fact it may be the hardest thing to engineer.
He only has to look to Valverde to see how quickly time can slip away. At the ripe old age of 35, his captain finally snared a Tour podium place in 2015, years after he began trying. And in doing so it was apparent that it meant everything to him.
“You could tell by the way I reacted it was if I won the Giro itself,” Valverde said at the time. "It’s nothing short of incredible."
“We have time to grow old. The air is full of our cries. But habit is a great deadener.” - Samuel Beckett, Waiting for Godot (En attendant Godot).
The reality for Quintana is this. It's not enough to wait out Froome and the Sky train at its peak. For as long as Sky continues to exist, he will face the same daunting task.
Froome will eventually be replaced with the latest Dave Brailsford creation (perhaps both Yates brothers) and the team will continue to support them with an endless supply of riders who would themselves be leaders on any other team.
Quintana is speaking as if he has all the time in the world, but as we know, it waits for no man.