The Conservative MP for Buckingham won 322 votes out of the 593 ballots cast. Fellow Tory Sir George Young MP came second with 271 votes.
Many Conservative MPs, who refused to clap when the results of the ballot were announced, greeted his appointment with disapproval, as Bercow is seen as being too close to new Labour.
But Bercow promised to cast aside his political views in his new role.
"My commitment to this house is to be completely impartial between members of one political party and another," he said.
He also told MPs that becoming speaker was the "greatest privilege" of his professional life.
Bercow has a particular interest in special education needs, partly because his young son suffers from a speech difficulty called verbal dyspraxia.
He was appointed by Children's Secretary Ed Balls to conduct a review into services for children and young people with speech, language and communication needs after he raised the issue more than 20 times in Parliament over 15 months.
This review was published in July 2008.
Bercow was also the front bench spokesman for education and employment in 1999.
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