Still, Ahmed said the parties disagree on the power-sharing at the level of local governments, but they are determined to solve the issue before the final signing of the document on August 5.
The war has killed tens of thousands, displaced some four million people and left the oil-rich country's economy in ruins.
The deal says that Kiir will head the government during the transitional period and Machar will return as First Vice President.
While Kiir said he was "committed" to the deal, he highlighted several challenges going forward, especially in accommodating a bloated government.
"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.
He disclosed that both sides signed the 2015 peace agreement amid multiple reservations besides intimidation from the worldwide community but expressed hope of successful peace this time with mediation efforts by Sudanese President Omar Al-Bashir backed by leaders under the East African bloc IGAD.
Under the agreement, the transitional cabinet would be composed of 35 ministers, including 20 ministers from the government, and nine from the Machar-led Sudan People's Liberation Movement-in-Opposition (SPLM-IO).
"I would urge. IGAD to focus after this on the implementation of the agreement", Machar said in his address. It has been wracked by civil war, which has seen ethnic cleansing and numerous atrocities, since 2013. "There are so many things need to be done".
President Kenyatta commended the Republic of Sudan for the progress made and reaffirmed Kenya's commitment to the restoration of peace, security and stability in South Sudan.