With 99% of the votes counted on Saturday, the Civic Democrats had 35.3% of the June 2-3 vote, compared to 32.4% for the ruling Social Democrats.
Earlier, a poll on state television gave the Civic Democrats, led by former businessman Mirek Topolanek, 38% of the vote in the first general election since the nation joined the European Union in 2004.
Vaclav Klaus, the president, will start talks with the Civic Democrats on Monday about forming the next government, the CTK agency said.
The Civic Democrats campaigned on a promise to cut taxes, reform pensions and weed out corruption.
Surveys showed that many voters still had mixed feelings regarding the conservatives' economic reform agenda but decided to punish the ruling Social Democrats of Jiri Paroubek for a series of sleaze scandals that have occurred during their eight-year tenure.
Paroubek, seeking a third election win for his party, was put on the defensive at the end of campaigning by allegations from a top police officer that he, his interior minister and police chiefs tried to block corruption and murder inquiries that implicated top party members.
Communists are set to become the third biggest party in the new parliament after the exit poll gave them 12%.
The Civic Democrats are expected to seek an alliance with the Christian Democrats and the Greens, both centrist parties that back large parts of their reform agenda.
If the Civic Democrats' victory is confirmed, the Czechs will follow Poland and become the second ex-communist country to elect a mildly eurosceptic government since the EU's eastward enlargement.