Noda defeated Japan's former internal affairs minister Kazuhiro Haraguchi and former agriculture ministers Hirotaka Akamatsu and Michihiko Kano.
He won 818 in the ballot in which the four candidates fought for the majority of 1231 votes, the Kyodo news agency reported.
The elections, in which Noda was widely expected to win outright, included votes by Democratic Party of Japan (DPJ) local assembly members and individual party members across the nation.
Noda, later expressed his willingness to carry out a cabinet reshuffle and take steps to shore up the economy with the aim of restoring the popularity of his government in the run up to the general election, which must be held within a year.
The public support for the ruling Democratic Party of Japan (DPJ) is very low, since Noda took the office last September.
As prime minister and leader of the DPJ -- currently the biggest party in parliament -- Noda has pushed through some unpopular legislation on doubling sales tax.
This, alongside general disenchantment with his once-popular party, has left many lawmakers fearing for their jobs in the general election.
However, with no credible alternatives the contest appeared as a formality for the premier.
The DPJ came to power in 2009 after five decades of almost unbroken rule by the Liberal Democratic Party, but its once-radical agenda was largely rejected.
