Community leader Jodie Belyea won the Victorian-based electorate on Saturday but Labor recorded a negative 3.5 per cent swing on a two-party preferred basis.
Dr Chalmers said the result showed community support for changes to stage three tax cuts, which redistributed them towards middle-income Australians.
But he said the government was not taking anything for granted despite the win.
"We're not complacent or carried away by the really great outcome," he told Sky news.
Treasurer Jim Chalmers says the government is not taking anything for granted. (Mick Tsikas/AAP PHOTOS)
"The Dunkley by-election was a vindication of the leadership the prime minister showed in making sure we could provide a tax cut to every Australian taxpayer but with a bigger emphasis on middle Australia."
Deputy Prime Minister Richard Marles conceded there were still takeaways for the government ahead of the May budget and next federal election.
Voters are due to go back to the polls before May 24, 2025.
"We will be very careful in hearing that message and we'll go through these results in a lot of detail to really understand what is being said here," he told ABC Radio on Monday.
"We want to learn everything we can from this result, I mean, it is a matter of historical fact that there tends to be swings against governments in by-elections."
Labor's primary vote went up almost one per cent but the Liberals gained a 6.5 per cent swing on the same measure.
Prime Minister Anthony Albanese said that result was due to right-wing parties such as One Nation not running a candidate.
"That explains the bump in the Liberal primary vote," he told ABC Radio.
"The Liberal Party under Peter Dutton, the lesson they've taken from the last election is to become more conservative, more right wing."
Late Labor MP Peta Murphy wanted gambling reform to be a big part of her legacy. (James Ross/AAP PHOTOS)
But Victorian Liberal senator Jane Hume said Saturday's result showed promising signs.
"By the time (the votes are fully counted) it may be the most marginal seat in the state and there were some real green shoots, I think, for the Liberal Party there for the first time in about a decade," she said.
"We always knew this was going to be a tough by-election for the Liberal Party; we haven't held the seat of Dunkley with its current boundaries ever before and at the last election our primary vote went down.
"We've certainly got our tails up."
Senator Hume said the result also signalled positive signs in other Melbourne-based electorates such as Kooyong and Higgins, which the Liberals lost in 2022.
"All of these seats are marginal and they are in the mix," she said.
"Like every election, we will target marginal seats and Dunkley is now a marginal seat."
The by-election in Dunkley was triggered by the death in December of Labor MP Peta Murphy, who had held the electorate since 2019.
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