Heavy police and army patrols circulated in the otherwise empty dirt roads of Juba on Wednesday. Shops and an outdoor market were burned to the ground, according to an Associated Press reporter at the scene.
The violence broke out in the wake of the death of John Garang, the charismatic leader of rebels who for 21 years fought against the domination of mostly animist and Christian southern Sudan by the Khartoum government in the mainly Muslim Arab north.
Garang died in a helicopter crash on Saturday night, three weeks after he became vice-president under a peace deal that calls for a power-sharing government between the north and the south.
The government and Garang's own Sudan People's Liberation Movement say the crash was an accident, but outraged southerners - some believing the government was behind the death - have rioted in Khartoum, Juba and other cities.
In Juba, 1200km south of the capital, angry southerners attacked Arab-owned shops and homes, chasing northerners through the streets and killing them, witnesses said. The witnesses spoke on condition of anonymity for fear for their lives.
Juba is a garrison town for the
In one case, two Arabs tried to seek refuge in a nearby camp set up for humanitarian workers, but police turned them away.
The two men were killed not far from the camp, Sudanese staff at the camp said, refusing to give their names for the same reason.
The staff said they knew of 18 people killed over the past two days.
Juba, a main front in the long civil war, is a garrison town for the northern Sudanese military. But it appeared the military and police held back from stopping rioters for fear of inflaming tensions with southerners in the town.
The impoverished town, the biggest in the south, has a population of about 350,000, most of them southerners - who are ethnic Africans, mainly animists and Christians. The town is surrounded by SPLM forces and is supplied from the north by air.
But the Arab Muslim minority holds most of the main businesses. Many of them were now fleeing. At Juba's airport, dozens of Arabs - mostly men - were lined up with baggage for flights back to Khartoum. Women and families appeared to have already left.
Juba is key to the north-south peace agreement. The town - which is mainly made up of thatched huts and stores - is due to become the capital of the autonomous southern region.
The central government is supposed to reduce its military presence and allow the SPLM's fighters to enter as a force parallel to the military.
Garang, whose body is currently at a SPLM base called New Site, is due to be buried in Juba on Saturday, and President Umar al-Bashir has announced he will attend.