Judge Ricardo Brousset's joint rulings included 30 years' house arrest for former lieutenant colonel Humberto Orbegozo and 23 years for Pedro Paz Avendano, for the crimes in the Andean city of Huamanga.
Brousset issued an arrest warrant for the men, who did not appear for their sentencing.
Administrator Colonel Roberto Saldana meanwhile was acquitted. Colonels Carlos Briceno and Carlos Millones had their charges dropped due to health problems.
The hearing Thursday into Friday detailed kidnappings, torture and executions of the 53 people at the Domingo Ayarza barracks, known by the nickname "Los Cabitos" in 1983. It had an oven where bodies were incinerated.
A truth commission report said the 1980-2000 civil conflict left 69,000 people dead.