Two female contenders, Sanae Takaichi, 60, and Seiko Noda, 61, dropped out after the first round.
The winner of the party poll to succeed unpopular Mr Suga, who is not seeking re-election after just one year in office, is almost certain to become premier because of its majority in parliament's lower house.
Mr Kishida must call an election by 28 November and faces the task of rebuilding an economy staggering from the COVID-19 pandemic, but his consensus style will help him consolidate power within the factious ruling party.
Mr Kishida's victory is unlikely to trigger a huge shift in policies as Japan seeks to cope with an assertive China and revive an economy hit by the pandemic, with the soft-spoken MP highlighting the need to focus on reducing income disparity.
He shares a broad consensus on the need to boost Japan's defences and strengthen security ties with the United States and other partners including the QUAD grouping of Japan, the US, Australia and India, while preserving vital economic ties with China and holding regular summit meetings.
Specifically, Mr Kishida wants to beef up Japan's coast guard and backs passing of a resolution condemning China's treatment of members of the Uyghur minority. He wants to appoint a prime ministerial aide to monitor their human rights situation.
Mr Kishida said deregulation during the reform era in the early 2000s widened the gap between the haves and have-nots and that former prime minister Shinzo Abe's "Abenomics", which sought to fix tattered finances by achieving high growth and boosting tax revenues, did not result in benefits trickling down.
He has said fiscal consolidation would be a major pillar of his policy and in the past has voiced doubts over the Bank of Japan's ultra-loose policy, saying in 2018 that stimulus cannot last forever.
With the economy suffering from the COVID-19 pandemic, Mr Kishida reversed course to say the BOJ must maintain its massive stimulus, saying Japan likely would not raise a sales tax rate from 10 per cent "for about a decade".
He stressed the need to distribute more wealth to households, in contrast to the focus of Abe's "Abenomics" policies on boosting corporate profits in the hope benefits trickle down to wage-earners.