The crime by the "Jackals" paramilitary group includes the massacre of 41 people in the Kosovo village of Cuska where Serbs rounded up villagers, robbed them, separated women and children from men, locked the men in a house and set it on fire.
The crime in Cuska and three other villages in western Kosovo in May, 1999, were among the most brutal of the 1998-99 conflict that killed 10,000 people after independence-seeking Kosovo Albanians rebelled against Serbian rule.
The civilians were attacked with an aim to force them to leave Kosovo and never return, judge Snezana Nikolic Garotic said. Civilian property was destroyed so they would have nothing to return to, she added.
The indictment said that the soldiers "have shown exceptional brutality and ruthlessness" by shooting people in their backs, and then setting them on fire "to prevent determining their identity."
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The war crimes prosecutor's office said it would appeal the acquittals and demand harsher punishment for some defendants.
War crimes trials in Serbia are part of efforts by authorities to deal with the wartime past as the state seeks EU membership.