His comments come as famine has been declared in parts of the African nation, where an estimated 100,000 people are already starving according to the UN.
The UN also reports that 275,000 children are severely malnourished and more than 5 million people are urgently in need of food, agricultural and nutritional assistance.
The country, which is the newest nation on earth, has also been devastated by three years of civil war.
In a Facebook post, Archbishop Justin appealed for new humanitarian corridors for aid to reach people in need.
"We stand prayerfully alongside the South Sudanese people and their leaders," he wrote.
"We pray for those on the ground who are delivering humanitarian assistance, that there will be an opening up of humanitarian corridors for the aid that is so desperately needed."
Archbishop Justin is currently visiting several countries in Africa. In the Facebook post, he said that he had already met a number of people who had fled violence in South Sudan and sought refuge in neighbouring countries.
"I've seen first-hand the consequences of the volume of refugees attempting to cross the borders to find safety, and the crisis facing those neighbouring countries as well as those in South Sudan."
The Archbishop appealed for prayers to those suffering and for "the Holy Spirit to comfort those who need it most."
Aid charities are already working in South Sudan. John Birchenough from the Christian charity, CAFOD recently returned from South Sudan and spoke with Premier about the situation there.
"I was meeting people who hadn't eaten for days who were going out foraging for food and that was in an area of relative peace so you can imagine how it is in other areas.
"Many of the people we talked to had fled from neighbouring areas. One woman I spoke to fled twice – she fled from the north of the country to Jubba and then there was fighting there so she fled for a second time," he said.
Birchenough added that he was moved by the way people were helping their neighbours despite their situation.
"People with so little were still trying to help others who came to their door looking for help and that touched me very deeply."
The famine is the first to be declared since the Somalian famine in 2011. More than 250,000 people died from starvation over a two year period.