The Czech Republic currently holds the European Union's rotating presidency and Barack Obama, the US president, is to visit Prague next week for talks with Czech and European leaders.
The ruling coalition, made up of Topolanek's right-wing Civic Democrats, the Christian Democrats and the Greens had 96 seats in the lower house of parliament.
The Social Democrats and Communists had 97 seats and needed the backing of at least four of the seven independent members to bring down the government.
The vote passed with the help of four deputies, formerly members of the ruling coalition, who had become independents.
Franticek Bouc, a Czech journalist, said the collapse of the government had come after sustained pressure by the political opposition.
"This cabinet has been very weak from the beginning in terms of the support it had in the parliament. After the general elections in 2006 it only had very fragile support in parliament. The opposition had already tried four times before to initiate through a vote of confidence the collapse of this cabinet.
"The Czech Republic, along with other countries in eastern and central Europe, are now trying the fight the economic crisis. Even though Topolanek's cabinet did very good moves, it was always very easy for the opposition to say 'look, they are incompetent and doing things wrong'. Today was not about the Czech voter, it was about the parliament."
Earlier, Topolanek had said it would be "irresponsible" for the independents to back Tuesday's censure motion at a time of crisis and ruled out the idea of a caretaker government until the end of the Czech EU presidency.
The latest motion followed charges that an adviser to Topolanek had tried to pressure state television into dropping a programme critical of a former Social Democratic deputy who now backs the coalition.
It is not immediately clear who will be picked by Vaclav Klaus, the Czech president, to form a new government.
If three attempts to form a government fail, early elections must be called.