CAS was asked to rule in the case after the Spanish athletics federation (RFEA), of which Dominguez is a former vice president, absolved the athlete of any wrongdoing in February 2014.
She had been provisionally suspended by the International Association of Athletics Federations (IAAF) and banned for four years in July 2013 after anomalies were detected in her biological passport that suggested she had used a prohibited substance or method.
The IAAF appealed the RFEA's decision and the World Anti-Doping Agency (WADA) filed its own appeal, with the two procedures later consolidated and referred to the same panel of CAS arbitrators.
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CAS ruled that "none of the explanations offered by the RFEA or Marta Dominguez were sufficient for the Panel not to be comfortably satisfied by the scientific evidence presented by WADA and the IAAF’s experts that an anti-doping rule violation had occurred".
"Accordingly, the Panel set aside the RFEA Decision and found Ms Dominguez guilty of an anti-doping rule violation," they said in a statement on their website (www.tas-cas.org).
As well as decreeing a three-year suspension, CAS also ordered that all Dominguez's competitive results from Aug. 5, 2009 until July 8, 2013 be disqualified.
Dominguez, now 40, beat Russia's Yuliya Zaripova into second in the race in Berlin on Aug. 17, 2009, with Milcah Chemos Cheywa of Kenya third and Gulnara Galkina, another Russian, fourth.
As well as the latest case, Dominguez, who is a senator for Spain's ruling People's Party (PP) and one of Spain's best-known athletes, was caught up in a police sting dubbed 'Operation Greyhound' in 2010.
She was one of 14 people taken in for questioning by the Civil Guard suspected of involvement in the trafficking of illegal drugs and crimes against public health but was later cleared of all charges.
According to Spanish media, Dominguez's defence at CAS consisted of raising doubts about the reliability of the biological passport.
She also argued that the fact she suffers from hyperthyroidism may have been responsible for any anomalies.
(Reporting by Iain Rogers, editing by Alan Baldwin)
