Cycling's governing body, the UCI, said in a statement that the 38-year-old Paolini, who rides for Russian team Katusha, was tested on July 7, the day of the fourth stage.
Paolini, who was a support rider for teammates Joaquim Rodriguez and Alexander Kristoff at the Tour, can request a "B'' sample to be tested after he was notified "of an adverse analytical finding of cocaine," the UCI said.
In accordance with UCI anti-doping rules, Paolini has been provisionally suspended. Cocaine is among a class of stimulants whose use is banned only in competition.
"The presence of cocaine has been detected in a sample," the team said. "Bearing in mind the anti-doping regulations, the team will wait until the analysis of the B sample has been conducted before taking any further action or making any further comment."
Paolini, who was 168th overall after Friday's seventh stage, 46 minutes and 41 seconds behind race leader Chris Froome, won the Gent-Wevelgem one-day classic earlier this season.
Katusha spokesman Philippe Maertens said Paolini "was shocked" when finding out about the result.
Tour de France director Christian Prudhomme could not immediately be reached for comment.
In March, the one-day classics specialist posted his first victory in nearly two years after overcoming heavy wind and rain and conditions to win Gent-Wevelgem.
His previous victory came in May 2013 when he claimed a stage win at the Giro d'Italia.
During his career, he also secured podium-finishes at the world championships, in the Tour of Flanders and in Milano-San Remo.
The UCI and the French anti-doping agency are working together in handling the Tour de France testing program, which includes targeted controls.
On the eve of the race start in the Netherlands, questions were raised when Vincenzo Nibali's Astana teammate Lars Boom was allowed to start the race despite a low cortisol level, which can indicate cortisone doping but is not a conclusive proof of doping.
AP Sports Writer Jerome Pugmire contributed to this report.