The tribunal found Hebron resident Hossam Qawasmeh guilty of "participating in the kidnapping and murder of Naftali Frenkel, Eyal Yifrach and Gilad Shaer on June 12," an Israeli army statement said.
The court will later pronounce sentence on Qawasmeh, who the army said confessed to organising the abduction with Marwan Qawasmeh and Amer Abu Eisha.
He financed the operation through money he obtained from his brother Mahmud, said by the charge sheet to be a Hamas operative who had been expelled to Gaza.
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The deaths, which Israel immediately blamed on Hamas, triggered a series of events that led to the devastating 50-day war in Gaza last July and August that killed almost 2,200 Palestinians and 73 people on the Israeli side.
The boys were shot almost immediately after their abduction, and their bodies were discovered on June 30 near where they were snatched.
The army says the kidnapping was orchestrated by Qawasmeh, a senior Hamas militant who sent the other two, both of whom had spent time in prison for their involvement in Hamas, to carry out the abduction.
The pair were later killed by the army in Hebron.
Israel rounded up hundreds of Hamas members in the West Bank in a mass arrest operation, prompting an uptick in rocket fire from the Gaza Strip, where Hamas is based, and setting the stage for an Israeli operation in Gaza.