Besides President Kenyatta, the signing of the agreement was also witnessed by Sudan President Omar al-Bashir, Uganda's Yoweri Museveni, and Ismail Omar Guelleh of Djibouti.
The opposition coalition of the South Sudan Opposition Alliance (SSOA) and other opposition factions who had earlier rejected the deal due to differences over the contents of the accord have all signed the pact.
President Uhuru Kenyatta has applauded parties to the South Sudan conflict for signing an agreement on the outstanding issues on governance and security geared towards restoring peace in Africa's youngest nation.
Some opposition groups, however, have not signed the deal as they are dissatisfied with the power-sharing arrangement.
"I call on everyone as a leader of South Sudan that this agreement which we have signed today should be the end of the war and the conflict in our country", said President Salva Kiir.
South Sudan President Salva Kiir confirmed on Friday he is more than ready to make peace with rebels by inking the final peace deal on Sunday in the Sudanese capital.
South Sudan's almost five year conflict began after Kiir accused his sacked vice president Machar of plotting a coup against him in 2013.
Manchester City chase visa for Douglas Luiz amid transfer frustration
After finishing fifth last season, Chelsea might have been expected to be more active in the transfer market this summer. I'll be happy if we arrive at the end being there [in contention] in April and May.
Kiir and Machar's factions have already agreed on a permanent ceasefire and withdrawing of their forces from civilian areas, in talks mediated by Khartoum in series of dialogues hosted by Bashir.
Sudan helped broker the agreement.
The deal further stipulated a transitional national legislative body composed of 550 members, with 332 from the government, and 128 from the SPLM-IO.
A 2015 peace agreement was shattered when the warring parties renewed fighting in July 2016 in the capital, forcing rebel leader Riek Machar to flee into exile. "Where will I get this?"
Machar said, "there is no option but peace. we have to focus after this stage on implementing the agreement that if we don't implement, we will all be failures".
The conflict has been fuelled by divisions between the Mr Kiir's Dinka and Mr Machar's Nuer ethnic groups.
The South Sudanese President also said that he was "going to sign", the agreement.