The former champion has been tasked with helping his young compatriot Fabio Aru but he was not even able to do that during the fifth stage, falling backwards in one of the short but tough climbs of the day in the Massif Central.
Nibali's coach Paolo Slongo hinted on Tuesday that his rider could make his own move at some point if he had the legs. Clearly, however, he is already out of contention. The hierarchy at Astana, which was causing audiences to speculate, has become much clearer.
"We were saying at the beginning that we did not have any indication on his form. Apparently he has not recuperated from the Giro," said Astana team manager, Alexandre Vinokourov.
Nibali is hoping to peak towards the end of the Tour, which finishes on July 24, and hold his form until the Olympics road race in Rio on August 6.
That meant that he could have been a danger for the big guns in the final week of the Tour providing he had been able to hang on with the best in the opening part of the race.
Last night, however, he lost eight minutes and 38 seconds to defending champion Chris Froome (Sky) and the other favourites, after finishing the stage 13 minutes and 45 seconds behind stage winner, Greg van Avermaet (BMC).
"He was in a bit of a crisis today," said Vinokourov.
"But the most important thing is that Fabio is here (with the best)."
Nibali took 15 days off after the Giro.
"I wanted to stay near the front with Fabio but I didn't have the legs and I wasn't having a good day so I really let it all go.
"It's not easy to race here after the Giro. We've all said many times that Fabio is racing for the Tour, so we're here in support of him.
"Today it would have been nice to be alongside Fabio but it wasn't my day. I'm fine with this. I don't have any regrets. I have a big goal for myself and that's what I'm aiming for now." - Vincenzo Nibali
The 26-year-old Aru is riding his first Tour de France and expectations are high for the Sardinian climber, who won his maiden Grand Tour last year when he prevailed in the Vuelta Espana.