Vladimir Churov, a State Duma deputy from the Liberal Democratic Party of Russia, was elected by a 13-2 vote.
Churov, the only nomination for CEC chairman, was proposed by CEC member Yelena Dubrovina.
"This person is not constrained by stereotypes that have built up in our system," she said.
Alexander Veshnyakov, 54, the first post-Soviet election chief in the new democratic Russia, was effectively dismissed by President Putin when his name failed to appear on the list of new CEC candidates, nine months prior to parliamentary elections and a year before presidential polls.
Churov said there will be less politics in his work as CEC chairman.
"The principal difference between me and Alexander Veshnyakov is that I am less likely to comment on election law and more inclined to get things done," he said.
Veshnyakov, whose term as Russia's top election official expired March 26, told reporters that "the commission's chairman, deputy chairman and secretary will be elected by secret ballot."
The Central Election Commission is formed by both houses of parliament and the president, each proposing five candidates.
Veshnyakov said he has no plans to go into politics when his term expires.
He refused to comment on his future job, but said he had received a number of interesting proposals and invitations to join three political parties.
Veshnyakov opposed Putin's administrative reform of 2000-02, which replaced governors elected to the upper house by popular vote with regional representatives appointed by the president, and abolished gubernatorial elections.
Veshnyakov also opposed a Kremlin-sponsored law that scrapped the 20% minimum voter turnout requirement and absentee ballots, but approved of a ban on "negative" television campaigning.
Another initiative of the pro-Putin parliament that Veshnyakov refused to accept was a bill introducing additional grounds for denying candidates' registration, which he said could be used to deny registration to any undesirable candidate.
