Blagojevic was sentenced to 18 years in prison by the International Criminal Tribunal for the former Yugoslavia (ICTY) based in The Hague.
“The trial chamber finds Colonel Blagojevic guilty of complicity in genocide by aiding and abetting genocide,” judge Carmen Maria Argibay said as she read out the verdict.
In April last year Blagojevic’s superior, Bosnian Serb general Radislav Krstic, became the first man found guilty of genocide.
On appeal he was sentenced to 35 years in prison for his role in the massacre of more than 7,000 Muslim men in Srebrenica following the fall of the eastern Bosnia enclave in July 1995.
The massacre is considered the worst single atrocity on European soil since World War II.
It is the first episode in the bloody 1992-95 Bosnian war that has been found to constitute genocide by the UN court.
The chamber said that while it could not be established that Blagojevic knew of the executions at the time he assisted the forcible transfer of Muslims, which accounted for his relatively light sentence.
In reaching the verdict the judges recalled the scale of the executions.
“Between 14 and 16 July, the men were blindfolded, put on buses and taken to nearby fields where group after group of terrified Bosnian Muslim men were executed.”
Blagojevic’s co-accused Dragan Jokic was sentenced to nine years for crimes against humanity and war crimes.
Last year Momir Nikolic and Dragan Obrenovic, two other Bosnian Serb officers listed on the same indictment, pleaded guilty to charges of crimes against humanity and were sentenced to 27 and 17 years respectively.
Six men accused over the massacre are still at large including Bosnian Serb wartime leaders Radovan Karadzic and Ratko Mladic.
Former Yugoslav leader Slobodan Milosevic is currently on trial in The Hague on over 60 charges of war crimes including a genocide charge over the Srebrenica massacre.