At the close a 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. Then he got down on his knees and kissed the leaders' feet one by one.
The pope usually holds a ritual washing of the feet with prisoners on Holy Thursday, but has never performed such a show of deference to political leaders.
"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.
The spiritual retreat brought together 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.
South Sudanese Vice President Rebecca Nyandeng Garang said Francis' actions moved her profoundly.
"I had never seen anything like that. Tears were flowing from my eyes," she said.
South Sudan, gained independence from Sudan in 2011 and in 2013, 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 12th, opposition leader Machar is expected to return to South Sudan and once again serve as Kiir's deputy.
However, the agreement, which was signed in September in Khartoum, the capital of neighboring Sudan, has been met with delays, missed deadlines and continued fighting with key aspects still not implemented.
A military coup in Sudan on Thursday fueled worries in South Sudan that the toppling of longtime President Omar al-Bashir could derail the already fragile peace deal.
"Sudan has helped us with the peace deal. We hope that the new system will also focus on the agreement, ensuring that it will be implemented," said opposition leader Machar, who attended an evening prayer vigil for peace, held at Rome's church of Santa Maria in Trastevere.
AP writer Sam Mednick in Juba, South Sudan contributed.
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