The 30-year-old used a product containing ephedrine, a substance prohibited in more than minor concentrations by the World Anti-Doping Agency, to treat saddle sores, without consulting the Cervelo Test Team doctor.
The news means 2008 Tour champion Carlos Sastre's squad, which features Britons Jeremy Hunt and Daniel Lloyd, are set to start the Tour with only eight riders as it is not yet clear if Florencio will be replaced.
A Cervelo Test Team statement issued tonight read: "Rider Xavier Florencio will not start for Cervelo Test Team at the Tour de France this year.
"Although he was nominated for the team, the team has decided to immediately withdraw him due to a violation of internal policies.
"Consistent with the team's internal values, Test Team riders are required to obtain permission from the team's medical staff before they can use any supplements or medication.
"This evening, the team learned that Xavier Florencio has been using a substance containing ephedrine to treat a saddle discomfort.
"This substance was not cleared in advance with the medical staff.
"This usage without clearance violates the internal policy.
"The rider is suspended from competition until the team can make a final determination based on all the facts.
"At this point there is no information yet on whether the rider can or will be replaced."