"They caught two men who had no identification documents and took them to a military post. The men suffered torture there," Chief Judge Lieutenant-Colonel Adil Karokaro told the tribunal in Jayapura.
The You Tube video showed the men being tortured while the soldiers tried to find out about an arms cache.
"The victims had their hands and legs bound and their faces stepped on. One victim had his genitals burnt with a burning stick and was also suffocated with a plastic bag," Karokaro added.
The men, who were found guilty of insubordination, said that they might appeal against their verdicts. All had confessed to their crimes and said they regretted their actions.
Human rights activists have repeatedly criticised human rights abuses carried out by Indonesia's military. The United States last year agreed to open military links with Indonesia's special forces, a move which was widely criticised.