Prime Minister Anthony Albanese confirmed the money alongside federal Infrastructure Minister Catherine King and Premier Jacinta Allan on Thursday.
"Next week's budget will contribute an additional $3.25 billion for this project, bringing the Commonwealth investment up to $5 billion," Mr Albanese told reporters at Watsonia.
"My government will work with state and territory governments across the board on nation-building infrastructure, such as this project here, which is really fitting in a missing link in the Victorian road network. "
The major road project in Melbourne's east was originally tipped to cost $10 billion when it was unveiled in 2016 and priced at $15.8 billion in the 2017 business case.
In December, a new price tag of $26.1 billion was revealed.
Construction is under way on the 10km-long connection between the Western Ring Road and an upgraded Eastern Freeway, which is set to be as wide as 20 lanes in some sections and includes 6.5km of tunnels.
The extra money from the federal government will take its contribution to the project to $5 billion.
The state government signed a $11.1 billion deal in 2021 with Spark consortium to build, operate and maintain the the project's tunnel toll road.
It is expected to cut travel times between Melbourne's north and southeast by up to 35 minutes and take 15,000 trucks off local roads each day when completed in 2028.
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