The court It also ordered the government to pay 51 head of cattle to the relatives of the local journalist who was killed in the raid.
The hotel owner is also due to receive compensation for the destruction and looting of his property.
The court case was widely seen as a test of will by the government of President Salva Kiir to bring accountability in the military that has long drawn accusations of widespread rights violations and a culture of impunity.
Gen. Briano delivered his judgment before a group of diplomats, aid workers and officials who have filled the military courtroom Thursday to hear the ruling.
The charges stem from the attacks in the Terrain Hotel in Juba in 2016, when dozens of soldiers broke into the compound, killed a local journalist and gang-raped five international aid workers while UN peacekeepers nearby did not respond to pleas for help