The International Cycling Union said the rider returned an adverse analytical finding from an out-of-competition test conducted on June 18.
The 32-year-old had been selected in the Trek-Segafredo's nine-man squad for the Tour - which starts in Dusseldorf on Saturday - as a support rider for Alberto Contador, but has now been provisionally suspended.
"The Union Cycliste Internationale (UCI) announces that Portuguese rider Andre Cardoso was notified of an Adverse Analytical Finding (AAF) of Erythropoietin in a sample collected in the scope of an out-of-competition control on 18 June 2017," a UCI statement said.
"The control was planned and carried out by the Cycling Anti-Doping Foundation (CADF), the independent body mandated by the UCI, in charge of defining and implementing the anti-doping strategy in cycling.
"The rider has the right to request and attend the analysis of the B sample. In accordance with UCI Anti-Doping Rules, the rider has been provisionally suspended until the adjudication of the affair."
Erythropoietin, commonly known as EPO, is a drug that boosts production of red blood cells and in turns speeds the delivery of oxygen to muscles.
Cardoso's team issued its own statement which read: "To our cycling family, we have some disappointing news to share.
"It is with deep disappointment that we have just learned that our rider, Andre Cardoso, has tested positive for a prohibited substance. In accordance with our zero tolerance policy, he has been suspended immediately.
"We hold our riders and staff to the highest ethical standards and will act and communicate accordingly as more details become available."
Cardoso has completed seven grand tours in his career but this summer was to be his Tour de France debut.
Trek-Segafredo subsequently announced that veteran Spanish rider Haimar Zubeldia would take Cardoso's place in the Tour squad.
