The Pope kissed the feet of President Salva Kiir and opposition head Riek Machar. Also present were Kiir's three vice presidents. The pope kissed the feet of all of them.
At the closed two-day retreat in the Vatican for the African leaders, the pope asked South Sudan's president and opposition leader to proceed with the peace agreement despite growing difficulties.
'I express my heartfelt hope that hostilities will finally cease, that the armistice will be respected, that political and ethnic divisions will be surmounted, and that there will be a lasting peace for the common good of all those citizens who dream of beginning to build the nation,' the pope said of South Sudan in his closing statement.
South Sudan gained independence from Sudan in 2011 but two years later the country plunged into a bloody civil war, which left at least 400,000 people dead.
The two-day Vatican meeting was held a month before the end of the shaky peace deal's pre-transition period. On May 12, opposition leader Machar is expected to return to South Sudan and once again serve as Kiir's deputy.