Labor was predicted to have at least 46 seats on Saturday night, to govern in its own right.
"Congratulations @DanielAndrewsMP, what a great win," Prime Minister Anthony Albanese tweeted soon after the result became clear.
Earlier in the evening, former Strictly Ballroom star Paul Mercurio clinched the seat of Hastings for Labor from the Liberals.
But it was not the only seat to change hands, as former professional tennis player Sam Groth declared victory in the seat of Nepean on the Mornington Peninsula, prying it from Labor early in the count.
"I certainly wasn't expecting them to call it this this early in the night, I'm very happy," Mr Groth said.
"I haven't had the chance to have a beer yet."
Labor's Chris Brayne won the seat in 2018 with a one per cent margin.
Senior Liberal Georgie Crozier told Seven she was disappointed in early voting.
"We've worked hard, we had what I felt was a very strong message, which clearly the Victorian public haven't taken," the coalition health spokeswoman said.
Earlier on Saturday, some Victorians had to hand-write votes on blank ballot papers as a number of centres ran out on election day.
The Victorian Electoral Commission confirmed the ballot paper shortage on Twitter on Saturday night.
"In the interim voters were provided with blank ballots, with candidates' names handwritten on the ballot. This is an acceptable approach in this situation," the commission said.
Polls closed at 6pm on Saturday, after weeks of early voting in which nearly two million Victorians pre-polled.
After voting opened on Saturday, Premier Daniel Andrews urged Victorians to opt for a strong, stable, majority Labor government as polls pointed to the potential for a hung parliament.
Liberal Leader Matthew Guy, who steered the opposition to a crushing defeat at the 2018 election, said he was confident of victory despite the polls strongly favouring Labor.
Almost half of the 4.4 million enrolled Victorians had already cast their ballots at early voting centres or by post, leading to a warning from the electoral commission it could delay results on election night.
The premier broke with tradition to cast his ballot early on Thursday, voting outside his electorate of Mulgrave with wife Catherine and two of his children.
A Newspoll published on Friday showed Labor on track to return despite a swing against it of almost three per cent.
The coalition held 27 seats and needed to pick up an extra 18 to govern outright.