Some 111 out of 180 lawmakers participating in the vote have supported the move, with the country's head of government among them.
The parliamentary session was broadcast on the republic's television.
The decision was taken after the prime minister lost a confidence vote by the government on January 16.
The withdrawal of immunity will, in fact, mean the beginning of his criminal prosecution under fraud charges, following accusations against Andrej Babis and his closest associates, made by police several months ago. The charges include organizing a scheme to misappropriate 50 million korunas (about $ 2.4 million) by one of his companies from EU subsidy funds.
Babis, in turn, has denied all the charges against him.
However, it has not helped the top official, as not one of the country's parties wished to form a coalition with his ANO (YES) centrist movement after October's parliamentary election, citing the charges against him.