Stupar, who was first sentenced to 40 years in prison at a trial before the same court in 2008, was not responsible for genocide charges from his indictment, the court's appellate chamber, presided by Judge Azra Miletic, decided.
At the time when Serb forces committed atrocities in Srebrenica, Stupar had no real command over the second unit of the Serb special police, headquartered on Sekovici, the appellate panel said.
After he was sentenced in 2008 to 40 years in jail, the harshest possible sentence to be imposed by the Court of Bosnia-Court, the defence team for Stupar lodged an appeal.
The first verdict was quashed in September 2009, after which a retrial was held before the appellate chamber of the Court of Bosnia-Herzegovina.
The appellate chamber established that members of the second unit of the Serb special police had perpetrated war crimes in Srebrenica on 13 July. They were engaged in firing squads that executed captured Bosniaks in the village of Kravica near Srebrenica.
At least, 1,000 Bosniaks were executed in Kravica.
On 13 July 1995, the said unit of the Serb special police was under the command of Rade Cuturic and after he was wounded he was succeeded by Stupar on 14 July.
Cuturic died in the autumn of 1995.
Six Serb policemen from their unit have so far been convicted of the Kravica crime and have been handed down long prison sentences.