The 26-year-old entered Stage 17 in third place overall behind Chris Froome and Nairo Quintana. But he fell behind the peloton in the middle of the stage, with French television reporting he was suffering from a headache. He rallied briefly but appeared to be laboring to keep up.
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With around 70 kilometers to go, van Garderen stopped altogether and got off his bike, walking unsteadily back to the BMC team car as he was consoled by staff members.
Van Garderen finished fifth overall at the Tour in 2012 and 2014 and was eyeing a top-three finish this year after Froome posted a lead that is likely insurmountable earlier in the race.
