The balloting was forced when outgoing Prime Minister Alenka Bratusek resigned in May after losing a power struggle within her own political party.
The government of predecessor Janez Jansa, formed after an early vote in 2011, collapsed last year when he faced corruption allegations.
He was jailed last month in a bribery case unrelated to the scandal that brought down his government.
Analysts have predicted another coalition government and more uncertainty after Sunday's balloting.
The 50-year-old parliamentary consultant only formed the party in June, but swiftly gained popularity because of his untainted public record.
Cerar said upon casting his ballot that "people have lost trust in political parties."
"They know the crisis is still strong," he added. "The only possibility for ending it is to have new people, unburdened by past stories, enter politics."
Cerar is challenged by Jansa's conservative Slovene Democratic Party. Jansa received a two-year sentence in the bribery case involving an arms deal; he has sought to portray himself as the victim of left-leaning political opponents. Jansa said on his Twitter account that he was not granted a brief prison leave to vote.
The Social Democrats and the Pensioners' party are trailing behind.
Cerar has opposed the privatization of some of Slovenia's state-run companies, which is part of an EU-backed anti-crisis package.
The outgoing government froze the sale process of Slovenia's main airport and Telekom Slovenia until a new Cabinet is formed.
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