Contador succumbed to illness and injury during Sunday's ninth stage, quitting just over 80km into the 184.5km trek through the Pyrenees.
Slightly more than 100 kilometres (60 miles) from the end of Stage 9 from the Spanish town of Vielha to the ski resort of Arcalis in Andorra, the 33-year-old Spaniard stopped at the side of the road, hopped off his bike and got into the passenger seat of his team vehicle.
"Alberto had a bit of fever this morning", Sean Yates, the sporting director of Contador's Tinkoff team, said just before the withdrawal.
He went into the stage more than three minutes behind overall leader Chris Froome.
Two-time champion Alberto Contador pulled out with a fever midway through the stage.
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 vehicle several times.
It was clear that he was suffering on what was a baking hot day in the Pyrenees with temperatures reaching 35 degrees Celsius.
However, what made it surprising for some people was that Contador had actually attacked, alongside fellow Spaniard Alejandro Valverde, on the opening climb of the day.
"I will undergo tests to find out what is going wrong", Contador said.
"As he had attacked, he obviously wasn't feeling too bad but I guess he was still suffering from his injuries". Contador lost time in the uphill finish at Cherbourg in stage two before being distanced by his rivals towards the end of the hilly stage in the Massif Central on day five.
The result leaves him 3min 12sec adrift of Froome in 20th overall and 2min 38sec down on Kreuziger, who finished a strong fifth on stage eight and is 12th in the standings.
"It's a shame he's no longer in the race".
Froome said the Tour would be poorer for the Spaniard's absence. It would have made the Tour even more exciting than it already is.
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.
It was the second time in the last three editions of the Tour that Contador has been forced to quit due to injuries suffered in a crash.