The opposition requested the vote after a preliminary EU report concluded the subsidies amounted to a conflict of interest because he still formally controls the businesses.
Only 85 of the opposition lawmakers voted early morning Thursday at the end of an almost 19-hour debate to oust the Cabinet, well short of the 101 needed in the 200-seat lower house.
Babis' centrist ANO (YES) movement is in a minority government with the leftist Social Democrats with support from the Communist Party.
The opposition was boosted by recent massive street protests demanding the resignation of Babis.
Babis denies wrongdoing.
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