Under the new law, which was narrowly adopted with 102 votes in the 200-seat Czech parliament, the Government will return assets valued at €5.4 bn that were seized from the Catholic, Reformed, Brethren, Orthodox and Jewish communities in the 1940s and 1950s.
But the Government will stop paying clergy salaries.
Three months earlier the law was vetoed by communists and Social Democrats in the Senate upper house.
Under the new law, 56 per cent of church assets, valued at 75 billion Crowns (€3 bn), are to be returned from January, with 59 billion Crowns (€2.4 bn) provided in compensation for the rest over a 30-year period, during which an annual government grant to churches will be phased out.