The Victorian Greens have won their second seat in Parliament, the Victorian Electoral Commission (VEC) has confirmed.

Candidate Sam Hibbins wrested the seat from Liberal Clem Newton-Brown.

Mr Newton-Brown won 45 per cent of the first preference vote, but with preference flows from Labor the Greens took the seat with a margin of 262 votes.

Mr Hibbins said his win was the first time a Greens candidate has taken a seat from the Liberal Party.

"That there are people who may have voted Liberal in the past, are unhappy with the approach of the Liberal Government, both state and federal, their lack of action on climate change, their lack of an environment policy, their lack of action on renewables and will vote for the Greens when the alternative is presented," he said.

"Certainly the federal effect resonated here in Victoria and certainly in Prahran, certainly by those who you would classify as, perhaps, small 'L' liberals, those centre-right voters who do care about social issues and do care about the environment and are willing to change their vote because of it."

The Labor Party challenged the result and a recount was due take place this morning, but Mr Newton Brown has already conceded.

"10 days after the state election we now have a result for Prahran," he said in a statement.

"I congratulate Sam Hibbins for his victory and also acknowledge the strong campaign of Neil Pharaoh.

"It has been a roller coaster ride for us all as the lead changed frequently as new batches of votes were counted.

"It has been such a privilege to represent Prahran and I hope that the many people who have supported me over the years feel that I have made some positive contribution to both Prahran and the wider community."

Mr Hibbins said he was confident the result would stand.

"This is the result we were looking for," he said.

"We previously had a primary vote of under 20 per cent. We've now boosted that up by almost 5 per cent so we got a major swing towards us in this election.

"We said we were looking to overtake Labor on the three-party preferred and then to defeat the Liberals on the two-party preferred and that's exactly what we've done."

It gives the Greens two seats in the Lower House after Ellen Sandell won the seat of Melbourne.

Federal Greens Senator Sarah Hanson-Young tweeted that the win sent a message to the Abbott Government.

"Great win for progressives, marriage equality and the next generation," Senator Hanson-Young said.

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The inner-city electorate is the state's smallest seat.

It takes in the suburbs of South Yarra, Prahran, Windsor, Toorak and parts of St Kilda.