The president is impeached over allegations he handed out government contracts in return for bribes.
Mr Vizcarra said he would accept the vote, not take any legal action, and leave the presidential palace.
Manuel Merino, the speaker of Congress, is expected to assume the presidency until July 2021 - when Mr Vizcarra's term was due to end.
It is the second attempt over the last two months to oust the president.
Mr Vizcarra, 57, has previously denied allegations that he accepted bribes worth 2.3m soles ($640,000; £487,000) when he was governor of the southern Moquegua region.
Before the vote, he also warned that any impeachment could throw the country into turmoil as it grapples with a severe economic recession brought on by the coronavirus pandemic.
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But on Monday, 105 lawmakers voted in favour of the motion - 19 voted against it and another four abstained.
Several lawmakers sympathetic to Mr Vizcarra have spoken out against the decision.
"This is a coup in disguise. We need calm, but also a lot of citizen vigilance," said George Forsyth, a former mayor who is running in next year's presidential race.
An impeachment vote held on 18 September fell far short of gaining the necessary votes when only 32 lawmakers cast their ballot in favour of removing Mr Vizcarra.
The impeachment proceedings two months ago focussed on allegations that Mr Vizcarra had misused public funds, which he denied.
Mr Vizcarra became president in March 2018 after his predecessor in office, Pedro Pablo Kuczynski, resigned amid allegations of vote buying.
He has been embroiled in a bitter battle with Congress, which is dominated by rival parties, since he took office.
Last year, the president dissolved Congress arguing that lawmakers were obstructing his anti-corruption agenda.
A new Congress was elected in January but tension remains high between the legislative and the executive with Mr Vizcarra accusing lawmakers of fostering "chaos and disorder".
Presidential elections are scheduled for April 2021 and Mr Vizcarra is banned by the constitution from running for a second term.