Issa Sallet Adoum, Ousman Yaouba and Tahir Mahamat were accused of taking part in an attack by the 3R armed group in May 2019 in which 46 villagers in northwest CAR were massacred.
Prosecutors had requested life terms for the three, accused of slaughtering civilians in the villages of Koundjili and Lemouna on May 21, 2019.
In a statement, the court said the trio were guilty of murder, inhumane acts and humiliating and degrading treatment.
Adoum, as "military chief", was additionally convicted over rapes committed by subordinates and of war crimes.
The three were acquitted on charges of torture committed as a crime of war.
Defence attorney Manguereka Andre Olivier said the defendants would file an appeal against the ruling. They have three days in which to submit their petition.
Justice Minister Arnaud Djoubaye Abazene, speaking outside the court, said the ruling was a "triumph of justice" and "a strong signal... against impunity".
Two other major cases are also pending, in the CAR and in The Hague.
This marked the first-ever trial of the UN-backed Special Criminal Court, a tribunal of local and international judges.
The special court's mandate applies to war crimes and crimes against humanity dating back to 2003.
The tribunal was set up in 2015 with UN backing but struggled for years to get going in the face of logistical hurdles, lack of money and local hostility.
After a faltering start caused by a lack of defence lawyers, its first trial opened on April 25 to a panel of national and international judges, with prosecutors from the Democratic Republic of Congo, France and Togo.
Victims of the 2019 atrocity hailed the court's ruling, after years of despair about the prospects for justice in a country sapped by weak governance, poverty and other ills.
"We are very happy with the verdict -- it's a message to the murderers: sooner or later, justice will catch up with them," said Fernand Made-Djapou, a lawyer who acts as spokesman for an alliance of civilian plaintiffs.
"I was there at the attack on Koundjili, where my elder brother... was killed, along with 13 other people I knew," a 34-year-old man told AFP, speaking on condition of anonymity.
On September 30, the court announced that it had charged an army commander, Vianney Semndiro, with crimes against humanity, torture, rape, sexual slavery and "forced disappearance of persons".
The alleged atrocities were committed at the Bossembele military camp north of the capital, Bangui, between 2009 and 2013, during the regime of former president Francois Bozize.
Part of the secretive camp had been transformed into jails for "political" prisoners, according to international NGOs and journalists who visited the camp in 2013 after the fall of Bozize.
In a separate case, the International Criminal Court (ICC) in The Hague last month began the trial of Mahamat Said Abdel Kani, an alleged commander of the mainly Muslim Seleka armed group that ousted Bozize.
He faces seven charges of war crimes and crimes against humanity relating to atrocities at a police compound where suspected Bozize supporters were beaten and tortured.