Saying Kenya and Israel "face the same challenges" of terrorism, Netanyahu cited the 2013 attack on the Israeli-owned Westgate shopping mall in Nairobi in which at least 67 people were killed by four jihadist gunmen.
"We have also experienced similar attacks in our country," Netanyahu said. "Working together will help us defeat the scourge of this terror even faster."
On Monday the prime minister visited Uganda to commemorate the 40th anniversary of the Israeli raid on Entebbe airport in which his brother Yonatan was killed rescuing hostages held by German and Palestinian hijackers.
In Nairobi the Israeli leader promised to share intelligence and provide "direct assistance" aimed at saving lives. "There is a raging battle with terrorism," Netanyahu said.
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Relations between Africa and Israel have been strained over the years. In the 1960s the Arab-Israeli conflict drove a wedge between African countries, many of which were embroiled in liberation struggles, and the Jewish state.
Later, wars between Israel and its neighbours in 1967 and 1973 led North African nations to urge sub-Saharan African states to cut ties with Israel, which many did.
Today, Kenyan President Uhuru Kenyatta said the hatchet had since been buried.
"We have had difficult relations with Israel as a continent, but the world has changed and we can't live in history," he said. "We will find more ways to cooperate and our relationship can only become stronger."
"Israel is coming back to Africa and Africa is coming back to Israel," Netanyahu said, insisting that Kenya and Israel share "common opportunities" as well as threats.
On the eve of Netanyahu's tour Israel announced a relatively modest USD 13 million aid package to strengthen economic ties and cooperation with African countries.
Israel's business with Africa constitutes only two per cent of its foreign trade, leaving plenty of room for growth while demand for its defence expertise and products is rising.
It also sees African countries as potential allies, particularly at the UN and other international bodies, where it is regularly condemned over its occupation of the West Bank and blockade of the Gaza Strip.