In a secret ballot, the confidence motion was passed with 65 votes in favor, 11 against, one abstention and one vote invalid, Dalia Venceviciene, Karbauskis' spokeswoman, said.
Karbauskis had promised to undergo a confidence test following three elections earlier this year.
Saulius Skvernelis, the LFGU's candidate, failed to make it to the runoff after coming third in the first round of May's presidential election.
The party also finished third in the municipal and European Parliament elections
Karbauskis had vowed to win all three elections and pledged to step down in case of failure.
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