The endorsement means Kenya becomes Africa’s sole candidate for the race for the non-permanent seat for 2021-2022.
In a secret ballot cast in the morning, Nairobi garnered 37 votes against Djibouti's 13 in a second round of voting in which 51 of the 55 AU member states were present.
In the first round, Kenya missed the two-thirds majority threshold after winning 34 votes against Djibouti's 15 with two abstentions.
There were no abstentions in the second round of voting.
Kenya has been lobbying for the seat within the continent and globally. The country had garnered 33 ballots in a vote held on August 5 at the AU, falling short of the two-thirds majority rule required on substantial decisions.
The endorsement now gives Nairobi renewed impetus to campaign for a seat it had declared interest in 2018.
Traditionally, the AU had often reached the UNSC candidature decisions through consensus but Kenya and Djibouti failed to agree on who should step down.
Foreign Affairs Cabinet Secretary Dr Monica Juma said the vote was a show of confidence for Kenya to represent Africa’s agenda at the UNSC.
“This endorsement is an affirmation that Kenya has remained true to the decisions and aspirations of the African Union and confirms that it is a safe and dependable pair of hands,” she said in a statement on Wednesday.
“Kenya commits to the African brothers and sisters that we shall be a bold voice for Africa and shall steadfastly promote and defend the African position.”
Djibouti’s Ambassador to the African Union, Mohammed Idris Farah said his country conceded defeat and congratulated Nairobi for the victory.
But even with this endorsement from the AU, Kenya must also win at least two-thirds votes of the UN member states when the election is held in New York next year in June.
Traditionally, elections to all UN bodies are done through formal balloting even if candidates have been endorsed by their regional group or are unopposed.
While AU’s endorsement almost certainly guarantees Africa’s 55 votes, there is nothing that could prevent an African member country of the UN from refusing to vote for the candidate approved by the continental bloc.
But like the AU, sometimes tight races are resolved by withdrawal of contests, election of a compromise candidate or sharing the term. In 2016, for example, Italy and the Netherlands agreed to serve the 2017-2018 term, six months each.