The United Nations has warned of tension and the possibility of fresh fighting in Juba, where a ceasefire has held since late Monday.
A convoy of around 50 trucks escorted by machine gun- mounted armoured vehicles crossed the Ugandan border at Nimule to open up a secure corridor for fleeing civilians on the 200 kilometre Juba-Nimule road.
"We plan to go to Juba to extract 3,000 Ugandans stranded by fighting, but that number may grow as we will evacuate anyone who wants to leave," said Uganda's army chief Brigadier Leopold Kyanda.
"Why not? We have the capacity to support the government of South Sudan and we were there before," said the plain- clothed officer accompanying the convoy.
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The Ugandan army joined the conflict in South Sudan soon after it began in December 2013, fighting on the side of President Salva Kiir against a rebel force led by Riek Machar, now the country's vice president. The troops only pulled-out late last year.
While the situation remained calm in Juba today concerns remain that fighting might flare once again.
Four days of intense battles in the capital left hundreds dead and forced around 40,000 to flee their homes. Aid agencies are warning of a worsening humanitarian crisis with a lack of both water and food.
The recent violence in the capital echoed the fighting that triggered the civil war and marks a fresh blow to last year's deal to end the bitter conflict that began when Kiir accused Machar of plotting a coup.
Kiir is a member of the Dinka tribe, while Machar is a Nuer, and the dispute has split the country along ethnic lines and caused tens of thousands of deaths.
Machar's return with a 1,400-strong bodyguard meant there were two hostile armies in the city. A shoot-out between Kiir's and Machar's guard units triggered the fighting that began on Friday afternoon.