The appeals chamber at the International Residual Mechanism for Criminal Tribunal overturned their acquittals of involvement in the criminal plan and raised the sentences of Jovica Stanisic and Franko Simatovic from 12 to 15 years.
Neither man showed any emotion as Presiding Judge Graciela Gatti Santana passed sentence.
Stanisic was in court for the hearing, while Simatovic watched by video link from a UN detention unit.
The decision brings to an end the longest-running war crimes prosecution dating back to the Balkan wars of the early 1990s.
The length of the case underscores the complexity of successfully proving war crimes in international courts, amid international calls for perpetrators of atrocities during the current war in Ukraine to be brought to justice.
Stanisic, a former head of Serbia's State Security Service, and Simatovic, a senior intelligence operative with the service, are the only Serbian officials to have been convicted by a UN court of involvement in crimes in Bosnia.
Milosevic was put on trial for his alleged involvement in fomenting the bloody conflicts that erupted as Yugoslavia crumbled but he died in his cell in 2006 before verdicts could be reached.
Stanisic and Simatovic initially were acquitted a decade ago by the UN's Yugoslav war crimes tribunal but an appeals chamber later ordered a retrial. That case was heard by the residual mechanism that deals with unresolved cases from the Yugoslav and Rwanda tribunals.
Mechanism judges convicted the two Serbs in 2021 of involvement in crimes as paramilitaries overran the Bosnian town of Bosanski Samac in April 1992. But the judges cleared them, citing a lack of evidence, of similar crimes in other towns and villages in Bosnia and Croatia. They were each sentenced to 12 years imprisonment.
"The trial chamber is satisfied that the accused provided practical assistance which had a substantial effect on the commission of the crimes of murder, forcible displacement and persecution committed in Bosanski Samac and were aware that their acts assisted in their commission," Presiding Judge Burton Hall said when convicting Stanisic and Simatovic in 2021.
Both the defendants and prosecutors appealed.
At a hearing in January, Stanisic's lawyer, Wayne Jordash, told judges his client was "a bit player." He was, Jordash argued, "barely involved at all."
