The coalition, formed by three parties -- Civic Democratic Party (ODS), the Christian Democrats (KDU-CSL) and TOP 09 -- won 27.78 per cent of the vote on Saturday after almost all voting districts have reported results, reports Xinhua news agency.
The ruling ANO party led by Prime Minister Andrej Babis came second with 27.13 per cent.
The coalition of Pirates and Mayors took about 15.6 per cent of the vote.
Freedom and Direct Democracy (SPD) also made its way to the Chamber of Deputies, or the lower house of Parliament, with 9.56 per cent of the vote.
Neither the Czech Social Democratic Party (CSSD), the junior party in the current government, nor the Communist Party of Bohemia and Moravia (KSCM) made it above the five percent threshold to win seats.
It is unclear how a viable government will form since the former government, composed of ANO, CSSD, with support from KSCM, lost its majority.
Parties will now have to negotiate to form a government.
The election started on Friday and ended at 2 p.m. on Saturday.
This year, 5,242 candidates, nominated by 22 entities, competed for 200 seats in the Chamber of Deputies.
The election is significant as the Chamber of Deputies is the house from which the government is formed, and the house with the largest say in proposing and debating legislation.