Several lawmakers from the reformist camp broke ranks to vote against the head of their own List of Hope, Mohammad Reza Aref, who lost by 103 votes to 173.
February's election was widely seen as a referendum on last July's nuclear deal with world powers led by the United States, the signature policy of moderate President Hassan Rouhani.
Larijani's support for its passage through parliament kept him out of the fierce debate that saw a string of hardline opponents of the agreement lose their seats.
The remaining seats are held by independents and representatives of religious minorities who are expected to give Rouhani a working majority to pass key reform legislation that eluded him in the outgoing conservative-dominated parliament.
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Several leading reformists broke ranks to endorse Larijani in the runup to the speakership contest.
"Larijani can better direct parliament than Aref," Gholam Hossein Karbaschi, the leader of one reformist faction, the Construction Party, told the Shargh newspaper on Tuesday.
Reformist former health minister Massoud Pezeshkian was elected first deputy speaker.
Larijani, who turns 58 on June 3, is the scion of a famed Shiite clerical family and a regime veteran.
He was a prominent figure in the elite Revolutionary Guards during the 1980-88 war with Saddam Hussein's Iraq and served as state broadcasting chief from 1994 to 2005.
He stood unsuccessfully against hardliner Mahmoud Ahmadinejad for the presidency in 2005 and two years later resigned as secretary of the Supreme National Security Council in protest at his policies which triggered an economically crippling showdown with the West.