Residents in Juba fled as mortars and "heavy ground assault weaponry" were fired, the UN in Juba said.
More than 100 people are reported to have been killed in recent clashes between supporters of President Salva Kiir and vice-president Riek Machar.
A 2015 peace deal to end a 20-month civil war has failed to quell unrest.
James Gatdet Dak, a spokesman for Mr Machar, blamed Friday's violence on government troops.
"Our forces have been attacked at Jebel base. We hope it will not escalate," he told the AFP news agency.
The violence is the first since Friday, when a half-hour gun battle with heavy weapons and artillery killed more than 100 people. Some estimates put the death toll at about 150.
A South Sudanese journalist told the BBC that reporters counted at least 100 bodies, inside and outside the presidential palace's compound.
Friday's exchanges were apparently sparked by a shootout between Mr Kiir's and Mr Machar's bodyguards. The two men met at the presidential palace on Friday.
South Sudan, the world's newest country, marked its fifth anniversary of independence from neighbouring Sudan on Saturday in lockdown.
The country is so short of money that no official anniversary events were planned.
Tens of thousands died and millions were displaced in the civil war that split Sudan five years ago.
Heavy exchanges of gunfire have erupted near the UN building in South Sudan's capital after days of fighting between government troops and former rebels.