Two-time champion Contador climbed into the Tinkoff team car with 100km remaining of the stage from Vielha Val d'Aran to Andorre Arcalis.
The Spaniard was three minutes 12 seconds down in 20th place overall going into the stage after two nasty falls on the opening two days compromised his performance.
A bout of sickness Sunday was the final straw and his team said he would now target the Tour of Spain later this year after his early exit.
Contador at least avoided the appalling conditions for the summit finish with driving rain and icy hailstones pummeling the riders.
Dutchman Tom Dumoulin, who had been in a long break which also included King of the Mountain leader Rafal Majka and home hope Thibaut Pinot, eventually secured his first Tour de France victory.
"This is a dream come true. I'm so tired that I can't even speak," he told the official Tour de France website.
Pinot was dropped on the final steep climb to Arcalis, but had the consolation of wresting the polka dot jersey from Majka, having made significant inroads on the eighth stage won in such thrilling style by Froome.
The major contenders for overall honors were then left to battle it out just over six minutes behind.
Colombian Nairo Quintana, considered the major threat to defending champion Froome with Contador sidelined, tried hard to drop the race leader, but it came to nothing.
At the finish, Froome, his British compatriot Adam Yates and Quintana crossed the line in the same time.
It left Froome 16 seconds clear of Yates in the standings, with Quintana in fourth at 23 seconds.
Ireland's Dan Martin, who launched some strong attacks on the ascent, has moved up to third overall as Spain's Joaquin Rodriguez lost time.
Froome acknowledged that the day had a sting in its tail in the terrible conditions for the first summit finish of the race.
"That was a tough old day out there. Really, really hard day," he told ITV Sport.
"Going from pretty extreme heat -- 35 degrees, really hot, stuffy weather -- to hailstorm at the finish, 10 degrees," he said.
Monday is the first rest day of the three-week Tour.