It puts an end to 13 years in power of her left-wing Workers' Party. Ms Rousseff denies the charges.
Sixty-one Senators voted in favour of her impeachment and 20 against, meeting the two-thirds majority needed to remove her from the presidency.
Acting President Michel Temer will serve out Ms Rousseff's term, which ends on 1 January 2019.
Mr Temer, from the centre-right PMDB party, is expected to be officially sworn in later on Wednesday.
Ms Rousseff had been suspended in May after the Senate voted to go ahead with the impeachment process.
She was accused of moving funds between government budgets, which is illegal under Brazilian law.
Her critics said she was trying to plug deficit holes in popular social programmes to boost her chances of being re-elected for a second term in October 2014.
Ms Rousseff fought the allegations, which she said amounted to a coup d'etat.