Two-time Tour victor Contador abandoned the Tour on Sunday's ninth stage, having twice crashed in the opening two stages before struggling with illness.
Contador was rumoured to be set to sign a contract with Trek-Segrafedo on the first Tour de France rest day.
Four times during the opening 80km of Sunday's stage, Contador was seen dropping back from the peloton to speak to his team auto.
But Contador was unable to keep up with the pace of the leaders and quickly dropped back to the pack before spending long periods of time deep in discussion with his team-mates and staff in the Tinkoff team vehicle. The question is not whether I have recovered, but if I can participate in top condition.
He went into the stage more than three minutes behind overall leader Chris Froome.
He had started the stage in a bright fashion, though, attacking alongside fellow Spaniard Alejandro Valverde to catch a group of early breakaway riders on the first climb.
He called it quits on the what was second of the day's four climbs in the Pyrenees.
"As he had attacked, he obviously wasn't feeling too bad but I guess he was still suffering from his injuries".
He had lost time on several stages as he struggled with his injuries.
"It's a shame he's no longer in the race".
Now 33, previously believed to be appearing in his final Tour de France - he's since said he hopes to continue racing in 2017 - Contador had come to the race hoping for one final victory at the sport's biggest race.
Contador, one of only six men with titles in all three grand tours (France, Italy, Spain), quickly faded away though and rolled down to his team auto several times. "It would have made the Tour even more exciting than it already is", said Briton Froome, two years Contador's junior at 31.