Pechstein, banned after her blood profile showed abnormal values early in 2009, has been trying to overturn her ban upheld in November by the Court of Arbitration for Sport in order to compete in next month's Vancouver Olympics.
The 37-year-old German had requested an interruption of her ban until the court had issued a final ruling, given the time constraints with the Olympics just weeks away.
"This decision comes as no surprise," her lawyer Simon Bergmann said. "We will now focus on the appeal. We obviously cannot enforce a participation in the Games but we can hopefully have the ban lifted."
Pechstein, her country's most successful winter Olympic champion who has won five gold, two silver and two bronze medals, has denied taking banned substances. She was not named in the German team last week.
"Now there is clarity," German Olympic Sports Union chief Thomas Bach told reporters. "We hope that now all eyes will now be on the German Olympic team that will go to Canada."
The International Skating Union imposed the two-year ban in July before CAS upheld it late least year.