Cross-discipline maverick Pidcock is due to protect his mountain bike Olympic title at the 2024 Games which start in just two weeks.
"A disappointed Tom Pidcock will not line up for stage 14 of the Tour de France today," Ineos said.
"Tom is experiencing symptoms of Covid-19 and under advice from our medical team will now return home to recover."
The 24-year-old was pipped to the line on the stage-nine run over gravel roads in the champagne region.
Pidcock entered Tour de France folklore in 2021 for his daredevil descent of the Galibier, before climbing doggedly through massed and hysterical crowds to an epic stage win at Alpe d'Huez.
The Leeds native who learned his skills racing to get to school on time is also a cyclo-cross world title winner.
Ineos staff have been wearing masks on the team bus this week.
UAE's Juan Ayuso pulled out for the same reason on Friday. After the stage FDJ team chief Marc Madiot said he expected mask protocol to be implemented throughout the peloton soon.
"Once you've got Covid in the house your chances are compromised," he said.
