This leaves many in South Sudan doubtful on whether the deal would end the 5-year civil war in the country.
The war erupted following a power wrangle between President Kiir and his former deputy Dr Machar.
Further said he agreed with al-Bashir to keep the talks in Khartoum in order finalize the remaining issues which are mainly the implementation matrix of the peace agreement and the timetable for the return of the opposition leaders as well as the troops' redeployment.
On July 25, the South Sudanese conflicting parties signed an initial deal of power-sharing and governance prior to signing the final document of the deal on Sunday.
It also stipulated that the transitional cabinet would be composed of 35 ministers from both the government and the opposition, including 20 ministers from the government, and nine from the Machar-led Sudan People's Liberation Movement-in-Opposition (SPLM-IO). However, Machar would be only the most senior of five vice-presidents under Kiir.
On Friday, Kiir said he believed the new peace deal between his government and the main rebel group would not collapse because it was not forced upon them like previous accords.
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"Last month the White House warned that "a narrow agreement between elites" would not solve the problems plaguing South Sudan".
"We are supporting any initiative to bring peace to South Sudan and we hope this process will continue comprehensively", US Charge D'affaires in Khartoum, Steven Koutsis, told reporters after Sunday's deal was signed.
Negotiations for the peace deal had been completed and any outstanding issues with his opponents would be settled after signing of the deal, Kiir said.
But he highlighted several challenges going forward, especially in accommodating a bloated government. Sunday's deal is the 12th ceasefire and second power-sharing agreement.
President Kenyatta appealed to the political leadership in South Sudan to secure the future of the region by commencing implementation of the agreement.
About 2 million South Sudanese have become refugees in neighbouring countries.