It also encouraged states in the region to prepare to send more troops to potentially bolster the UN presence in the country.
Members of the UN body in charge of peace and security met at UN Headquarters in New York to consider how to respond to the latest clashes between forces loyal to President Salva Kiir and opposition forces loyal to his deputy Riek Machar.
The fighting, which began last Thursday and continued over the weekend, has reportedly led to at least 150 deaths. The violence erupted as the world's youngest country marked its fifth anniversary of independence at the weekend.
In a strongly-worded press statement, the council condemned the escalation in fighting across Juba and expressed outrage at the attacks on UN compounds and protection of civilian sites.
UN Secretary-General Ban Ki-moon said he was appalled by the heavy fighting and said in a statement that UN compounds and protection of civilians' sites had also been caught in the crossfire. He said he was deeply frustrated by the renewed fighting.
Earlier this morning, UNMISS expressed outrage at the resumption of violence in Juba, which it said was severely impacting the civilian population.
In a press statement, the mission reported that heavy fighting in Juba town, including in close proximity to the UNMISS compounds at UN House Jebel and Tomping, had prompted approximately 1,000 internally displaced people to flee from the UNMISS protection of civilians site (PoC) into the UNMISS compound at UN House Jebel.
Both UNMISS compounds in Juba sustained impacts from small arms and heavy weapons fire, the mission reported.
The Security Council however urged South Sudan's government to demonstrate leadership, get back on course and commit to deliver lasting peace for the population in South Sudan.
A genuine commitment is now needed, said the statement, to a full implementation of last year's peace agreement, including a permanent ceasefire.
President Salva Kiir and his deputy Riek Machar signed a peace agreement for the formation of the Transitional Government of National Unity nearly a year ago, after two years of a bloody civil war that killed tens of thousands and displaced more than 2.2 million people. Implementation of the agreement took effect two months ago.
The Security Council says the two leaders need to "do their utmost" to control their troops and reduce tensions between rival factions.
The Council also called for all parties to allow the UN Mission in South Sudan (UNMISS) to continue delivering vital humanitarian aid, support and protection to civilians caught up in the fighting.
Meanwhile, Samantha Power, the United States representative at the UN Security Council said they have called for regional countries to begin preparing troops for possible deployment into South Sudan.
The US government announced it was withdrawing all non-essential staff from its embassy in South Sudan.