The slaying was the worst massacre on European soil since World War II.
The ruling upheld Friday said that in the chaos of the Serb takeover of Srebrenica, U.N. commanders no longer had control of the troops on the ground, and "effective control" reverted to Dutch authorities in The Hague.
Human rights lawyer Liesbeth Zegveld, who represented the Bosnian families, called the ruling historic because it established that countries involved in U.N. missions can be found legally responsible for crimes, despite the world body's far-reaching immunity from prosecution.
"People participating in U.N. missions are not always covered by the U.N. flag," she said.
But Toon Heisterkamp, a Supreme Court Judge responsible for briefing the media, said the narrow focus of the case meant it was unlikely to have far-reaching effects.
Outside the courtroom, Nuhanovic said he was stunned by the ruling, which ends a 10-year legal battle and opens the door to compensation claims against the Dutch government.
"I was thinking about my family, they are dead for 18 years," he said. "It does not change that, but maybe there is some justice."
He added: "it should have happened years ago."
The Dutch government resigned in 2002 after the National War Documentation Institute blamed the debacle on Dutch authorities and the United Nations for sending underarmed and underprepared forces into the mission and refusing to answer the commanders' call for air support.
The government accepted "political responsibility" for the mission's failure and contributes aid to Bosnia, much of which is earmarked for rebuilding in Srebrenica. But it has always said responsibility for the massacre itself lies with the Bosnian Serbs.
The three men were among the last to be expelled, the 2011 ruling said, and by that time the peacekeepers known as "Dutchbat" for Dutch battalion already had seen Bosnian Serb troops abusing Muslim men and boys and should have known they faced the real threat of being killed.
"Dutchbat should not have turned these men over to the Serbs," a summary of the judgment said.
The Hague Appeals Court in 2011 ordered the families of the three slain men to be compensated, but no figure was ever reached, pending the outcome of the government's appeal to the Supreme Court.
Zegveld said the amount of compensation the families will receive is not important.
"It's far more important what's been decided today than any amount that will be established in the future," she said.
The Srebrenica massacre has turned into a national trauma for the Netherlands. Dutch troops returning home from Srebrenica faced accusations of cowardice and incompetence, although subsequent inquiries exonerated the ground forces.