Krstic denied the charges and plans an appeal
Radislav Krstic was sentenced to 46 years in prison, but spared the eight life sentences demanded by prosecutors.
The massacre in the Muslim enclave of Srebrenica - a designated UN safe haven - is regarded as Europe's worst atrocity since World War II.
"In July 1995 General Krstic, individually you agreed to evil. And this is why today this trial chamber convicts you and sentences you to 46 years in prison," said Judge Almiro Rodrigues.
Jim Landale, spokesman for the international tribunal, said the verdict "shows the victims of the Srebrenica massacre that the international community has not forgotten about them".
But some relatives of Srebrenica victims reacted with anger to the sentence, describing it as too lenient.
"Let him go and come back among us. We will give him a verdict," said Behara Hasanovic. "For 10,000 of our sons, only 46 years! His people have ripped my son from my arms."
Atrocity
Krstic, 53, is the first senior official linked with the massacre to be tried by the International Criminal Tribunal for the former Yugoslavia (ICTY) in The Hague.
He was second-in-command of the Bosnian Serb army's Drina corps, which spearheaded the attack on Srebrenica, an area that was officially under the protection of UN troops.
He looked tense and shocked as Judge Rodrigues read out the verdict.
His lawyer, Nenad Petrusic told reporters after the ruling that Mr Krstic would appeal against both the verdict and the sentence.
The general was seized by Nato troops in 1998. He pleaded not guilty to all of the charges.
In the five days after Bosnian Serb forces overran Srebrenica at least 7,500 Muslim men and boys are thought to have been killed.
Implicated
In a judgement that followed the 16-month trial - during which 116 witnesses were heard - the panel of judges found that Krstic was aware of and involved in the plans to kill them.
He was also implicated in the execution of the plans, and in attempting to hide the evidence afterwards, through the burial of the victims in mass graves.
In a long list of evidence, the tribunal cited orders given to General Krstic to deal with what were described as 3,500 "packages" - the remains of some of the victims.
The prosecution had asked for consecutive life sentences on each of the eight charges that included genocide, war crimes and crimes against humanity.
Responsibility
During his trial, Krstic said he was acting on the orders of other generals.
They include Ratko Mladic who, along with wartime leader Radovan Karadzic, has been indicted for genocide for his alleged part in the massacre.
Both men remain at large and are the court's most wanted fugitives following the extradition of former Yugoslav President Slobodan Milosevic to The Hague in June.
The BBC's Gabriel Partos says one reason for the 46-year sentence may be that judges want to keep life imprisonment - the tribunal's severest punishment - for those considered ultimately most responsible.
In the case of Srebrenica, that is expected to be kept in reserve for General Mladic - assuming, of course, that he is first captured, and then found guilty.