Kenyatta said they also discussed how they can increase trade between the two countries and connectivity on the African continent which is critical to industrial development.
President Uhuru Kenyatta's handlers were left red-faced Thursday after the head of state was momentarily blocked by the door of his official vehicle.
President Uhuru Kenyatta and his South African counterpart Jacob Zuma have expressed mutual desire to strengthen relations between their host countries for the benefit of their nations and peoples.
"It will enable us to create the jobs that our young people require", said Kenyatta.
A flight carrying the President left Jomo Kenyatta International Airport (JKIA) moments before noon.
"We are very pleased that President Kenyatta found time to come to South Africa as we celebrate our 106-year birthday‚" he said.
"We have also had the opportunity to discuss regional issues that are to do with mutual interest, matters of peace and security".
Presidents Kenyatta and Zuma said the two countries' ruling parties - Jubilee and the ANC - would begin working together. "I have had the opportunity to brief [President Zuma] on South Sudan", he said, adding that the leaders also discussed the slave trade of African migrants in Libya.
Kenyatta's discussion with Zuma will focus on bridging the balance of trade which is now highly in favor of South Africa.
Kenyatta said the relationship between South Africa and Kenya was already strong but they both want to take it further.
According to a statement from Kenyatta's office, he would meet with deputy president Cyril Ramaphosa on Friday.