The attack at the Terrain Hotel in the capital was one of the worst on foreign aid workers since South Sudan was plunged into conflict in 2013.
Eleven soldiers were on trial but one was set free due to the lack of charges against him.
The court said the government must pay $4,000 to each rape victim.
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.