Nevertheless, when Sky's Chris Froome put down the power on the short climb into Mûr-de-Bretagne, the only one of the favourites to fall behind was 2014's winner, Nibali.
Astana's team captain slipped backwards as the small group sped up the two-kilometre wall that averages 6.9 per cent. Frenchman Alexis Vuillermoz (AG2R La Mondiale) won the stage 10 seconds ahead of Froome's group, and 20 ahead of Nibali.
The Italian slipped 10 seconds behind Sky's yellow jersey leader and now sits 13th, at 1-48 minutes. Tomorrow comes the team time trial, and then the race heads into the mountains.
"To many it's not [a good sign], but what does that mean?" team manager Giuseppe Martinelli said at the base of the climb where Astana had parked its bus.
"It was a day where he couldn't perform like he wanted, but that can happen. We'll just let today go. We are not going to lose the Tour because of 10 seconds on the Mûr de Bretagne."
The signs were there early this year that Nibali might struggle to defend his title. Out of all the big favourites, he is the only one who came into the Tour without a major stage race win for 2015.
He complained of a complicated winter with the responsibilities of the Tour champion and an Achilles tendon injury. His Astana team also had to deal with five doping positives, two of which came from the professional WorldTour team that supports his ambitions.
Nibali fell on the back foot immediately in stage two of this year's race. He was left separated from the main group by a crash in front of him during the windy stage on the west coast of the Netherlands. He lost 1-21 to Froome and Alberto Contador (Tinkoff-Saxo), and on the Mur de Huy on stage three, he and the others lost another 11 seconds to Froome.
He tried to turn it around on the cobbles in Northern France, but he could not break his rivals. He appeared close to breaking point himself when he snapped at Froome for a crash in the final kilometre of Thursday's stage, although he did later apologise for this reaction.
What today's result will mean for him psychologically, ahead of a team time trial and the big mountains in the Pyrenees, remains unknown.
"It doesn't help him mentally, but his head is not one of the normal ones like the rest of us have," Martinelli said.
"He has something else — otherwise, he wouldn't be a champion."
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