Xisto Barros, 30, and Cesar Mendonca, 34, were on Thursday convicted of killing two civilians during the Suai church massacre in September 1999, in which Indonesian soldiers and their proxy militiamen stormed a church where refugees were hiding.
At least 31 people, including three Catholic priests, perished in the attack, which was among the bloodiest in the aftermath of the UN-organised independence referendum in which East Timorese voted to separate from Indonesia.
The two men also were convicted in a third murder in the village of Lookeu and the forced deportation of hundreds of villagers during a campaign led by the Indonesian military.
East Timor has indicted 440 Indonesian servicemen and militia members - most of them believed to be living in Indonesia - for human rights violations over the violence that left 1500 people dead and East Timor in ruins.
Jakarta refuses to hand over the suspects, and has said it will not respond to the indictments.
East Timor's government also has not pushed to have the defendants turned over, saying good relations with its large neighbour are more important for the country's future.
Jakarta has set up a special tribunal to prosecute Indonesians allegedly responsible for the violence, but the trials have been widely criticized as a sham.
Thursday's case was the last to be heard by the UN-sponsored Serious Crimes Unit that is due to close on 20 May. But the unit may have its mandate extended by at least six months based on recommendations by a UN fact-finding team looking into rights issues in East Timor.