The government, appointed by President Milos Zeman on July 10 after the previous premier was brought down by a spy and bribery scandal, needed a simple majority of votes from 193 lawmakers present to survive but won only 93, yesterday.
"I declare that the parliament has refused to voice confidence in the cabinet," parliament speaker Miroslava Nemcova said.
But the vote -- following nine hours of debate -- also showed that the centre-right parties from the governing coalition that was toppled in June can no longer count on majority strength in the 200-seat parliament.
This would lead to a snap vote within 60 days under the constitution.
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"Since the potential coalition of right-wing parties has crumbled, this seems to be the most reasonable solution," Tomas Lebeda, a political analyst at Prague's Charles University, told AFP.
The parliament already voted on its dissolution on July 17, following a proposal introduced by the left-wing Social Democrats who pollsters say would easily win a snap vote.
But their effort failed as they and their allies fell far short of the 120 votes required by the constitution.
"The TOP 09 caucus has decided to back an early election. Here's a petition calling for an extraordinary session on snap elections," Petr Gazdik, head of the caucus, said immediately after the vote.
Parliament speaker Nemcova from the right-wing Civic Democrats said before the vote that her party might also back snap elections.
"The option is still on the table, we never ruled it out," she said.
Lawmakers will start debating the dissolution today.
Social Democrat chairman Bohuslav Sobotka said early elections could take place in October.
Rusnok meanwhile said he would officially resign later this week but will lead the cabinet until early elections.
"I see the result as a very dignified loss," Rusnok told reporters.