Apart from the issues of trade and infrastructure, Presidents Kenyatta and Zuma also deliberated on regional peace and security, especially the South Sudan conflict and the "new slave trade in Libya".
"The fate of Africa is tied at the hip and the relationships should foster partnerships that are beneficial to the citizens", President Kenyatta said.
On his part, Kenyatta said his meeting with Zuma included talks on working together "for the mutual prosperity of our people", and improving connectivity on the African continent, which he said was critical to industrial development.
Kenyatta congratulated Ramaphosa with his "victory" of being elected as ANC president in December.
The President commended the ANC leader for following in the footsteps of the founding fathers of the ruling party, saying the message of unity resonates well with their ideals.
He said he also discussed bilateral issues which seek to foster greater partnership between the two countries with Ramaphosa, in his capacity as deputy president of the country.
It is the first time the President has set foot outside Kenya since he was reelected into office following a harrowing electioneering period and is expected to be in South Africa for three days. "What we need to do is to develop that relationship to a higher level to benefit our peoples and countries", said Ramaphosa.
Numerous South African companies have a presence in Kenya.
Ramaphosa said the exploitation of natural resources would create job opportunities for the youth.
A flight carrying the President left Jomo Kenyatta International Airport (JKIA) moments before noon.
Zuma is not well-liked by investors, who prefer his alleged replacement, leader of the ruling African National Congress (ANC) Cyril Ramaphosa.