A U.S. intelligence agent is assisting with the prosecution of suspects accused of killing a South Sudanese aid worker and raping his foreign colleagues.
The former vice president has left for a safe country in east Africa, according to a spokesman.
The rampage in Juba did not see UN troops, stationed only a mile away, intervene.
At least 120 cases of sexual violence and rape have been reported in the last three weeks.
Both sides call for calm as violence spreads fear that fragile peace is threatened.
Riek Machar was supposed to arrive in Juba on Monday, but a dispute over weapons has slowed him down.