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.
The government wants an independent African force to calm tensions in the capital Juba.
Rebel leader Riek Machar has still not returned to Juba after clashes in July.
The world's youngest country needs outside intervention to avoid all-out war.
At least 120 cases of sexual violence and rape have been reported in the last three weeks.
Taban Deng Gai says he will take up Machar's role until the rebel leader returns to Juba.
Fresh violence in the capital Juba has called the country's fragile future into question.
Hundreds have been killed after renewed fighting in the capital Juba.
Clashes in capital as vice president claims his residence was attacked by president's troops.
Both sides call for calm as violence spreads fear that fragile peace is threatened.
South Sudan's capital is hosting its first-ever film festival and the punters love it.
Conflict, poverty and hunger continue to blight the world's youngest country.
"Don't wait until we go the way of Sudan," the militant group warned.
South Sudan has one of the worst maternal mortality rates, and midwives are struggling to cope.
The world's youngest country has had a short but fraught history.
Governments are failing to resettle displaced people, leading to a growing annual total.
One week after he was due in Juba, the rebel leader is still nowhere to be seen.
More than 100 children were abducted from Ethiopia's Gambella region earlier this month.
Riek Machar was supposed to arrive in Juba on Monday, but a dispute over weapons has slowed him down.
Machar is due to return to the capital Juba on Monday after two years of civil war.