Suga, the son of a strawberry farmer from northern Japan who got his start in politics as a local assemblyman, has since 2012 held the key post of Chief Cabinet Secretary, acting as Abe's top government spokesman, coordinating policies and keeping bureaucrats in line.
He has the image as more of a behind-the-scenes operator than a frontline leader but rose in opinion polls after he announced his candidacy to succeed Shinzo Abe.
He won support from most LDP factions, outpacing his rivals.
Suga also won robust backing from LDP local chapters, where Ishiba had originally thought to be strong.
According to a tally by public broadcaster NHK, he took 89 votes from the chapter representatives versus 42 for Ishiba and 10 for Kishida.
Yoshihide Suga was scheduled to hold a news conference at 6pm (0900 GMT).
(Writers: Linda Sieg, Elaine Lies, Chang-Ran Kim, Chris Gallagher, Antoni Slodkowski | Editors: William Mallard, Lincoln Feast, Gerry Doyle)
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