Yukio Hatoyama was elected president of the opposition Democratic Party of Japan (DPJ), setting to steer the party to oust the ruling Liberal Democratic Party (LDP) in a key election this year.
Hatoyama won 124 ballots out of the total of 219, while the other candidate Katsuya Okada got 95 votes.
"I hope everyone can gather around the DPJ to complete a clean-up of Japan's politics," Hatoyama said after the election.
The vote came after 66-year-old Ichiro Ozawa's resignation as party chief on Monday over a political donations scandal.
The 62-year-old Hatoyama, the right-handed man of Ichiro Ozawa, had voiced he would follow the policies of Ozawa in order to accomplish a victory in the House of Representatives election which has to be held by September.
Recent public polls showed DPJ still enjoyed a lead over LDP as the preferred ruling party, despite the political fund scandal that forced Ozawa to resign.
The vote on the two candidates -- DPJ Secretary General Yukio Hatoyama and Vice President Katsuya Okada -- started at about 1:50p.m. Saturday, following the policy speeches and a debate between them.
Only DPJ members with Diet seats can cast ballots for the election. A total of 221 lawmakers -- 112 lower house members and 109 upper house members -- are thus eligible voters.