Marko Milosevic had been charged with violent behavior and causing severe bodily harm to
members of the opposition Otpor movement in 2000.
The court in Milosevic's hometown of Pozarevac based its decision on a lack of evidence and the expiration of the statute of limitations on the charges, the state Tanjug news agency reported.
Otpor has said it will appeal the ruling. It also said the decision was a result of Socialist Party demands to halt prosecution proceedings against Milosevic and his mother in exchange for joining a coalition government. The Socialist Party was founded by Slobodan Milosevic.
The trial was held in absentia as Marko Milosevic lives with his mother, Mira Markovic, in Russia. The two were granted political asylum by the Russian authorities in 2006. They are both wanted in Serbia for allegedly heading a cigarette smuggling ring in the early 1990s, which investigators say netted them several million dollars. The mother and son have denied the charges and have refused to return to their homeland to face trial.
The Serbian Justice Ministry said in late February it had issued an extradition request for Slobodan Milosevic's widow and son. Russia has said however that it sees no grounds for extradition.
Slobodan Milosevic, who led Belgrade into war and international isolation, culminating in the NATO bombing of the Yugoslav capital in 1999, died of a heart attack in custody in The Hague in March 2006. He passed away before a UN war crimes tribunal could pass its verdict on his role in conflicts that tore apart Yugoslavia.
Slobodan Milosevic's brother Borislav, a former Yugoslav ambassador to Russia, also lives in Moscow.