The film, first shown in December last year, caused an international furore and led to Russian athletes being suspended from international competition, triggering the deepest crisis in Russian sport since the boycott-hit 1980 Moscow Olympics.
The programme, which used secret recordings obtained by Russian middle distance runner Yulia Stepanova and her husband Vitaly, formed the basis of a hard-hitting report by the World Anti-Doping Agency, which prompted the International Association of Athletics Federations to suspend Russia last month.
Unless overturned, it means Russian athletes will be unable to take part in next year's Olympics in Brazil.
Russian sports officials disputed some of the report's findings and are working to get their athletes reinstated. Wednesday's court case, which is largely symbolic, appeared to be part of that campaign.
The court said it had ruled in favour of the Russian Athletics Federation (VFLA), which had filed the case, complaining that its honour and integrity had been impugned by the ARD documentary.
It ordered ARD, the film's producer, and Stepanova and her husband to pay fines of 3,000 roubles (£28.5) each, the Interfax news agency reported.
ARD declined immediate comment.
"Following the court's decision, ARD do not have to issue a retraction, as they are from Germany and the court process was in Russia," Valentin Balakhnichev, the former president of the VFLA, told Reuters in a phone interview.
"However, Russian law can now let us say that all the information in this film is a lie. This is a big step forward in defending our interests and our rights."
He said the ruling could help Russian athletes be reinstated.
(Additional reporting by Michelle Martin in Berlin; Editing by Andrew Osborn and Alison Williams)
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