Speaking at an open debate of the UN Security Council on the peacebuilding in Africa, the secretary-general said, "I am appalled by the scale of sexual violence documented by our Human Rights teams."
"We demand accountability for all atrocities and that the leaders of South Sudan commit to the peace process," he said.
The clashes between government and opposition forces took place in Juba, the capital of South Sudan, early this month, killing some 272 people, including 33 civilians.
The country again plunged into conflict in December 2013 after President Salva Kiir accused his deputy Riek Machar of plotting a coup, which the latter denied, leading to a cycle of retaliatory killings.
"Peace in Africa is a top priority," Ban said. "This is a cause of grave concern for all."
The secretary-general said that instability also persists in the Central African Republic, the Democratic Republic of Congo, Libya and Mali, and a number of other nations. But he added that in other countries, effective institutions are being built, and he noted that inclusive and accountable institutions are the cement that bonds States and citizens.
The secretary-general said that, despite praise for the Peacebuilding Fund in the recent peace and security reviews, it faces a desperate funding shortfall.
To deliver on the collective commitment to sustain peace, he asked governments to help the Peacebuilding Fund Pledging Conference in September to achieve the funding target of 300 million U.S. dollars.