The two Victorian polls in Werribee in Melbourne's west and Prahran in the city's inner east marked the first time Premier Jacinta Allan and new Opposition Leader Brad Battin were put to the test at the ballot box.
Labor traditionally holds Werribee but the party's primary vote was down 16.7 per cent when counting ceased on Saturday night.
The resignation of former treasurer Tim Pallas triggered the by-election.
As of early Sunday morning, Liberal candidate Steve Murphy had 29.04 per cent of the primary vote, with Labor's John Lister on 28.71 per cent.
But Mr Murphy (49.45 per cent) was trailing Mr Lister (50.55) on a two-candidate-preferred basis.
Meanwhile in Prahran - a Greens stronghold up for grabs after MP Sam Hibbins quit in disgrace following revelations he had an affair with a staffer - Liberal candidate Rachel Westaway claimed victory on Sunday.
This marked the first time the seat had changed hands in more than a decade.
Mr Battin said voters were becoming despondent because the Greens and Labor were "destroying their lives".
"They're sick of the crime here in Prahran," he told reporters.
"They're sick of the cost of living, their rents going up. They're sick of the congestion."
Victorian Greens leader Ellen Sandell blamed the loss on preferences and the by-election's timing.
"Obviously it's not the result we would have liked but with the unofficial Labor candidate sending their preferences to the Liberals, those Labor preferences have handed the seat to the Liberals this time," she said.
The Victorian Electoral Commission said a recheck count of votes would be conducted on Monday.
"This is a routine process after any attendance election, which involves rechecking each district ballot paper for correct counting and formality," a spokesperson said.
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