Ms Werner was on track to secure more than 60 per cent of the primary vote on Saturday night and was headed toward a two-party preferred vote of 69.8 per cent ahead of Greens candidate Tomas Lightbody (30.2 per cent).
"Thank you for entrusting me with this honour," she told volunteers and supporters at Ringwood Bowls Club as she declared victory on Saturday about 8.30pm.
"I will do my best to give my all every single day to fight for you and to serve our wonderful community."
The former youth pastor secured preselection after failing to reclaim the nearby seat of Box Hill for the Liberals in November when Labor was returned to government for another four years.
State Opposition Leader John Pesutto said Ms Werner's emphatic win was a warning shot to the Andrews Labor government.
"There will be an earthquake going off inside the Labor Party," he said.
Mr Pesutto said Victorians were sick of cost of living pressures, taxes, incompetence, and integrity scandals.
"The people of Warrandyte have been the voice of all Victorians tonight," he said.
"They have said loudly, enough is enough."
Mr Pesutto had denied the vote in Warrandyte would be a test of his leadership of the Liberal Party, which has experienced internal disputes in the nine months since he stepped into the role.
The by-election was triggered by the retirement of veteran Liberal MP Ryan Smith, who released a resignation press release in July without informing Mr Pesutto amid simmering factional tensions over the expulsion of first-term MP Moira Deeming.
Ms Werner opened her victory speech by thanking Mr Smith for his service to the electorate and the parliament.
"It is your shoulders I stand on tonight," she said.
Ms Werner had been a virtual certainty to retain the seat for the Liberals over a field of mostly independents after Labor opted not to contest the by-election, although the final margin will be closely scrutinised.
The Liberals held Warrandyte on a two-party-preferred margin of 4.3 per cent ahead of Saturday's poll.
The seat hasn't fallen out of the party's grasp since 1988.
Despite the margin, Mr Pesutto said he wouldn't pre-empt the by-election result.
"No seat is safe in politics these days - we've learnt that in recent federal and state elections," he told reporters on Saturday.
"You have to fight for every single vote... and at no stage in this Warrandyte by-election have we taken any votes for granted."
Mr Pesutto said Ms Werner had mounted a strong case for voters.
"Nicole will be that strong voice," he said.
"She's grown up in the area, she's a local and she wants to be a strong advocate for the people she wants to serve."
Factional warring between the Liberals and Labor's federal by-election win in Aston, also on Melbourne's outer fringes, had set the scene for a potential battle over the seat.
But Labor ultimately decided against contesting, with nominations confirmed a week after the Andrews government suddenly cancelled the 2026 Commonwealth Games over cost concerns.
Saturday's poll was the first Victorian state by-election since 2017 when now-federal senator Lidia Thorpe snatched the seat of Northcote from Labor following the death of Fiona Richardson.
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