Jovan Petkovic, 33, who served as a guard at the Serb-run detention camp at Stara Gradiska, was charged with ill-treating Nevenka Preradovic, 53, a member of the Croatian National Guard, from June to September 1993.
Preradovic said in her testimony that Petkovic had raped her on a number of occasions, inflicting on her physical and mental pain.
In 1996 the county court in Pozega sentenced Petkovic in absence to 12 years's imprisonment.
Petkovic was arrested on an international warrant in Switzerland in June this year. However, in the re-trial at the Slavonski Brod court, Preradovic withdrew her initial statement.
The court found beyond a reasonable doubt that the accused Petkovic, a member of the police force of the self-proclaimed Serb state in Croatia, had served as a guard at the Stara Gradiska camp at the time relevant to the indictment and that Preradovic was suffering from the physical and mental aftereffects of her detention at the camp.
The court could not corroborate the charges alleged in the initial indictment, under which the accused was tried in absence, Presiding Judge Mirko Svircevic said.
Since there was no evidence other than the testimony given by Preradovic, the court decided to acquit the accused.
The court judgement is subject to appeal.
Petkovic, however, will remain in custody because he is a suspect in another war crimes case before the same court.