Punctures hurt Contador
The Saxo Bank-SunGard rider made it back into the leading group after a first puncture on the penultimate climb of the 157-km stage.
Contador then holed another tyre 2-km from the finish line to slip almost three minutes behind Dutch leader Bauke Mollema in the overall standings.
"I could not do anything about that," the 26th-placed Spaniard said, "so I chose to finish the stage calmly and I hope I will have more luck in tomorrow's time trial".
Contador is fighting to clear his name after testing positive for the banned substance clenbuterol during last year's Tour de France, a result he blamed on contaminated meat.
The Spanish cycling federation (RFEC) lifted an initial ban in February but the International Cycling Union (UCI) and the World Anti-Doping Agency (WADA) have appealed.