The vote paves the way for possible prosecution in a corruption scandal that has sparked huge protests in recent months.
Crowds outside Congress cheered to celebrate the news.
Prosecutors last week accused President Otto Perez Molina of masterminding a scheme to defraud the customs service of millions of dollars. He denies wrongdoing.
The resolution was passed by 132 votes in favor, well clear of the two-thirds majority needed to pass the motion in the 158-member congress.
Under Guatemalan law the president will be automatically removed from office if remanded in custody.
Otto Molina Perez’s former vice-president and a string of top officials have been force to resign over the scandal.
It comes as Guatemala prepares for presidential elections on September 6.
Investigators have alleged that officials received a cut from bribes paid by businesses seeking to evade import duties.
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