Pockets of violence broke out Thursday evening, and by Friday, soldiers loyal to Kiir exchanged heavy gunfire with others backing Machar, in a bloody skirmish that left almost 150 people dead by Saturday, according to Machar's spokesman, James Gatdet Dak.
CNN has been unable to independently verify the exact death toll.
The Indian Embassy in South Sudan advised its citizens "not to panic" and to stay indoors. Many of the UNMISS staff members are Indian nationals.
A U.N. base was attacked last week.
"We heard heavy artillery fire at the U.N. (base), and that continued for about an hour or so and then stopped. It was coming form the outer perimeters of the compound," said Shantal Persaud, acting spokeswoman for the U.N. mission.
Helicopter gunships were seen in the sky, and tanks rumbled through the streets. Under the peace deal, both government and opposition troops were stationed in Juba, a plan which many criticized because it put both forces in close proximity.
Kenya Airways, which operates two flights a day to Juba, said it was suspending all flights to the city because of an "uncertain security situation," while Britain's Foreign Office advised against all travel to South Sudan, saying "the security situation in Juba has deteriorated" since Friday.
Two weeks ago, fighting in the western city of Wau between government and opposition troops displaced at least 70,000, according to the United Nations.
The country is nearly out of money because its funds come almost exclusively from oil revenue -- the value of which has plummeted. People have become desperate. In lieu of payment, government soldiers have reportedly been allowed to rape women, a U.N. report said
South Sudan gained independence in 2011 after 98% of the population voted to break away from Sudan. The East African nation, the youngest country in the world, quickly fell into civil war that took on ethnic undertones.
In December 2013, soldiers from Kiir's Dinka ethnic group tried to disarm Nuer soldiers perceived to be loyal to Machar. Soldiers targeted Nuer civilians in the ensuing fighting, Human Rights Watch says.
The civil war was gruesome -- at least 50,000 were killed, more than 2 million displaced, and nearly 5 million people faced severe food shortages. Under a peace deal signed in August, Kiir is the president of the country and Machar is the first vice president, but the fighting hasn't stopped.