The 12 soldiers were tried in four groups at the military court in Yogyakarta.
Presiding Judge Lt. Col. Joko Sasmito told the court Thursday that Second Sgt. Ucok Tigor Simbolon, 36, had been found guilty of executing all four detainees and sentenced to 11 years in prison. Two other soldiers were sentenced to eight and six years for helping with the executions.
"Their actions have damaged the image of the Indonesian military," Sasmito said.
Prosecutors had sought 12 years for Simbolon, who could have received the death penalty, and eight and 10 years behind bars for the other two.
But a three-judge panel said it considered the soldiers' service time in the military and their confessions of wrongdoing in deciding on the sentences.
Simbolon seemed relieved after hearing the verdict, but declined to talk to reporters.
In a separate trial, five other soldiers were sentenced Thursday to 21 months in jail.
The verdicts for four other soldiers are scheduled to be handed down Friday.
Kopassus troops have been implicated in a range of crimes and human rights violations over the years, but officials say they have worked to address the problem. The high-profile case is seen as a test of how far the military has come since the United States resumed some assistance to Kopassus three years ago after a 12-year break over human rights concerns.
Analysts say that violations by Indonesia's military are no longer widespread, but that there is limited accountability for abuses that do take place.