The military head of the UN peacekeeping mission was fired and the political head resigned over the incident.
UN investigators and rights group have frequently accused both the army and rebels of murder, torture and rape since the civil war began in 2013, and say the crimes almost always go unpunished.
The three-year conflict has fractured the country along ethnic lines - Kiir is an ethnic Dinka, Machar is a Nuer - and forced a quarter of the country's 12 million population to flee their homes.
Source: News agencies