Netanyahu's contender Danny Danon won 19 percent of votes, while six percent of voters abstained, the radio said.
Vote-counting continued into the early hours of Thursday following the party's elections a day earlier.
Interior Minister Gilad Erdan and Knesset (parliament) Speaker Yuli Edelstein have been chosen among other leading party members to represent the Likud in the upcoming Knesset elections, slated for March, the broadcaster said.
Last month, Netanyahu called early elections, citing difficulties in leading the state with his outgoing government.
The outgoing prime minister dismissed two leading members of his cabinet – justice minister Tzippi Livni and finance minister Yair Lapid – earlier, prompting the collapse of his coalition government.
Israel held its last general election in January of 2013. General elections must be held every four years in case there is no decision to hold snap elections.