The Sicilian was one of many riders who struggled to cope with the persistence of Sky's pressing at the head of the yellow jersey group on the Col de Joux Plane, and less than halfway up the day's final climb, Nibali opted to continue at his own tempo.
"I didn't even know how to explain it myself. I sat up on the final climb when I saw that I wasn't going to be able to stay with them," Nibali told reporters as he pedalled gingerly from the finish line to the Liquigas team hotel in Morzine. "I went up at a steady pace after that, I treated it almost like a training session, what can I say.
"I didn't feel great early on when we went up the first climb at a decent pace, but then little by little, I began to unblock a bit after that, so I expected to be better in the finale."
Nibali opted to forgo the Giro d'Italia this season in order to focus his energies for his tilt at the Tour podium. After enjoying a hugely consistent opening phase of his campaign, with victory at Tirreno-Adriatico, as well as podium finishes at the Tour of Oman, Milan-San Remo and Liège-Bastogne-Liège, Nibali has yet to rediscover the same vim after returning to action at the Tour of California last month.
"In California, I felt really bad but I looked to finish it because I knew it would do me good for the Tour," Nibali said. "I couldn't even say myself what was wrong. Since I went to California, I just haven't been going well. I don't know what's up, maybe I just didn't manage the journey well."
In spite of his showing on Saturday, Nibali was determined to take solace from his experiences last season, when he turned a low-key performance at the Giro del Trentino before battling his way onto the podium at the subsequent Giro d'Italia.
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"It's not the first time I've been in this situation," he said. "Last year at Trentino, I wasn't really great at all and then in the end at the Giro d'Italia I was going well. I have faith in my ability."
Like the injured Andy Schleck (RadioShack-Nissan), who withdrew from the Dauphiné early on Saturday's stage, Nibali stressed that he still has three weeks in which to fine-tune his condition ahead of the main event in July.
"I'm not worried, I know there's still a lot of time," he said. "I have to go into the mountains again and do a bit more work. It's not like I had a crisis today, I just didn't feel great. I still have some work to do."
As Nibali unclipped outside the lobby of his hotel, Daniel Mangeas' breathless tones could be heard in the background, reverberating through the streets of Morzine. The veteran speaker was excitedly describing the scene as Bradley Wiggins mounted the podium to receive another yellow jersey, while Cadel Evans (BMC) waited in the wings to collect the green jersey of points leader.
"The guys who are up there in GC are clearly going well and have a state of form that makes you think that they can go well at the Tour," Nibali said. "But let's not forget that there's still some way from here to the Tour. I'd rather go badly here than at the Tour."
Barry Ryan was Head of Features at Cyclingnews. He has covered professional cycling since 2010, reporting from the Tour de France, Giro d’Italia and events from Argentina to Japan. His writing has appeared in The Independent, Procycling and Cycling Plus. He is the author of The Ascent: Sean Kelly, Stephen Roche and the Rise of Irish Cycling’s Golden Generation, published by Gill Books.
