The result was expected because the coalition of Social Democrats, Christian Democrats and the centrist ANO movement, led by Finance Minister Andrej Babis, enjoys a comfortable majority in Parliament's lower house.
The no-confidence vote was called by three center-right parties after the parliament, in a vote that included ANO lawmakers, extended a tax break for rapeseed-based biofuels last week.
Andrej Babis, one of the richest Czechs, has been accused by the opposition of being biased because one of the companies he owns is a major bio fuel producer.
Babis, who employs about 35,000 people and has bought two of the country's four national mainstream newspapers, has long been under fire from other parties for being in charge of tax policy, state enterprises, tax inspection and other regulatory roles while also being a media, farming and chemicals entrepreneur.
Babis said he did not benefit from the tax break totaling up to 9 billion crowns for all firms by 2020.
The Czechs use tax incentives to meet their EU targets for usage of renewable fuels.
Prime Minister Bohuslav Sobotka supports the tax breaks, saying they help farmers.