The talks between the two presidents, and a number of Cabinet ministers, took almost two hours while the media waited for them outside the residence.
Kenyatta's call was a preliminary working visit, said Zuma.
"He has just come so that we could have some consultations and look forward to his state visit in the first half of this year. We want to strengthen our relations, take them to a higher level," he said.
Zuma said they had discussed issues affecting the African continent during the meeting.
He said some of the issues included the recent reports of a slave trade in Libya and South Sudan's civil war, which was now in its fifth year.
Kenya election discussed
"The South Sudan issue is quite a challenge to all of us. The kind of new slavery taking place in Libya is an issue that Africa cannot allow to happen again. It's an issue we believe we need to give serious attention to," he said.
It was the first time that Kenyatta had visited South Africa since he became the president of Kenya in November last year.
Zuma told the media that among the issues they had also discussed was the outcome of the October Kenya election.
Kenyatta won the re-run of the Kenyan elections, which was boycotted by the main opposition group.
Kenyatta, who won by a huge margin after he received 98% of the votes, faced no significant challenge after opposition leader Raila Odinga refused to participate, claiming the election would not be free or fair.
Kenyatta had also won the presidential vote on August 8 last year, but that election was later nullified by that country's Supreme Court due to a string of irregularities.
Working towards 'mutual prosperity'
"We talked about that as well because there are things that we believe need to be done right in the continent, particularly the respect of our democracies that we have all accepted," Zuma said.
Zuma revealed Kenyatta would also be part of the ANC's 106th birthday celebrations in East London on Saturday.
He said it was important for African political parties and leaders to meet and discuss how they can forge working relationships.
Kenyatta said he would make his official state visit to South Africa "during the first quarter of this year".
About the meeting on Thursday, he said: "We had the opportunity to exchange views on a number of issues largely pertaining to how we can strengthen and deepen the relationship between our two countries; how we can work together for the mutual prosperity of our people, increase trade between ourselves and how we can also improve connectivity in our continent, which is critical to our industrial development [and] which will enable us to create the jobs that our young people require."