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The upgrade, from Fulton Hogan, is expected to be completed by May.
The federal government is chipping in $565,000, with the rest of the funding coming from the City of Ballarat for the $1.1 million project.
The intersection, near the brand new Link Road roundabout, is a key part of encouraging new east-west links across the city - in 2020, Gregory Street West fully reopened to connect the Link Road to Gillies Street.
However, traffic chaos ensued when the Give Way priority was changed, leading to driver confusion and a backdown.
Since then, there have been regular crashes, with poor visibility and high speeds contributing to many of them - a driver was taken to hospital after a crash in January.
Council noted in a media release the intersection will remain open, but access from the Link Road will be blocked and detours will be in place.
Mayor Des Hudson said the aim was to make the intersection safer.
"As Ballarat continues to grow, we need to be able to accommodate the transport needs of our growing region both now and into the future," he said in a statement.
A second roundabout, at the intersection of Warrenheip Road, Eureka Street, and Navigators Road, is almost complete, with council stating it's expected to be finished by mid-March.
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Elsewhere, the state government's Keeping Ballarat Moving upgrade at the corner of La Trobe Street and Wiltshire Lane is still unfinished, with traffic lights yet to be switched on as of Wednesday morning.
Roundabout construction works at the Ballarat-Maryborough Road exit on the Western Freeway are also continuing, and expected to be finished by October.
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