"The decision was adopted," said deputy parliament speaker Tomio Okamura in a 111-69 vote.
Police have charged Babis with fraud, alleging the 63- year-old Slovak-born chemicals, food and media tycoon pulled his Stork Nest farm out of his sprawling Agrofert holding to make it eligible for an EU small-company subsidy before eventually putting it back in the holding.
Babis told parliament on Friday that the request was politically motivated and labelled the Stork Nest case "a purpose-built pseudo-cause", insisting the police had "no direct or indirect evidence that I committed a crime."
But Czech President Milos Zeman has said he will give Babis a second chance to form a new cabinet. If needed, a third and final try to form a government falls to the parliament speaker, who is currently a member of Babis's ANO movement.
Campaigning on an anti-corruption, anti-euro ticket, Babis's ANO (YES) scored a landslide win in October's general election, but Babis could not put together a majority cabinet after partners turned their backs over the fraud charges.
Yet the Czech Republic's future government is also hanging on the outcome of a presidential run-off election on January 26-27.
The pro-Russian Zeman is seeking re-election after clinching pole position in round one last weekend, setting up a final round against pro-European Jiri Drahos, a former academic, who has said a prime minister facing police charges was a problem for him.
Babis told the DNES daily, which his company owns, on Thursday he wanted his second cabinet named by Zeman, whose term of office expires on March 8.
Babis added that if Drahos wins the vote, he might refuse to name him as premier which could result in "destabilisation and a crisis,".
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