The state recorded 12,755 new COVID-19 infections on Friday, including 5345 from PCR tests and 7410 from rapid antigen tests.
Friday's death toll is the highest the state has seen since Victoria's second wave, when 59 fatalities were recorded on September 4, 2020.
It also comes two days after 35 deaths were reported.
"Our thoughts of course are with those 39 families, those 39 groups of friends, this is a significant loss," Health Minister Martin Foley told reporters.
The state is managing 101,605 active cases, while hospitalisations with COVID-19 have fallen by 69 to 988 patients, down from 1057 on Thursday.
There are 114 people in intensive care, a decrease of three, with 40 of those on a ventilator.
Mr Foley said Victoria's outbreak "seems to have stabilised" and the state's hospital services, currently subject to a code brown alert, would be turned back on once it's safe to do so.
"We've seen almost 40 people pass away in the most recent reporting period, this is a really significant challenge for our healthcare system," he said.
"Our hospitals, our GPs, our pharmacists are all under pressure like never before. When it's safe to do so, we will turn the system back on."
More than 35 per cent of Victorians aged over 18 have received a COVID-19 vaccine booster, with 23,252 doses administered at state hubs on Thursday.
Victoria will roll out booster shots for people aged 16 and 17 as soon as the Australian Technical Advisory Group on Immunisation approves the third dose, Mr Foley said.
A vaccination booster blitz for children aged five to 11 will begin this weekend, with 15 primary schools to offer pop up vaccine clinics and some state-run hubs to accept walk ups.
Ahead of students beginning Term 1 on Monday, Mr Foley said two million rapid antigen tests had been sent to schools, with another 4.6 million "on the way as we speak".
Twice weekly testing is recommended for all primary and secondary school students and staff, as well as early childhood education workers.
Meanwhile, the state government announced 13 organisations will share in $1.67 million from a Food Relief Financial Reserve funding round, to deliver goods to Victorians doing it tough due to the pandemic.
Organisations receiving the funding include OzHarvest, FareShare, Foodbank Victoria and SecondBite, as well as local foodshare groups in Geelong, Bendigo, Mildura, Shepparton and Warrnambool.
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