Gippsland and the Yarra Ranges have been hit with rising flood levels overnight, and people in the Traralgon area are subject to an evacuation order.
Emergency services are surveying the damage overnight, having predicted rising flood levels in the Yarra River at Yarra Glen, the Thomson River near Sale and Traralgon Creek near Traralgon.
Anyone living, working or holidaying in the Traralgon Creek area was ordered to evacuate before nightfall on Friday. An emergency warning just after 5pm said major flooding was possible at Traralgon town.
Traralgon Creek is expected to reach a 'major' flood level of 4.8m by Saturday morning.
"We are expecting to see another 80-100mm of rain over the Traralgon catchment later today and throughout the night," SES chief officer operations Tim Wiebusch said.
Emergency advice issued just before 7pm for the Sale region said the Thomson River at Sale Wharf was at 2.4m and rising.
The South Gippsland Highway is now closed between Sale and Longford.
Residents along the Yarra River from Millgrove to Coldstream are advised to evacuate if it becomes necessary.
Victoria has been relentlessly lashed with gusty winds and heavy rainfall since Wednesday night and two people have died in the dangerous conditions.
A young woman was found in a vehicle in floodwaters at Glenfyne 200km southwest of Melbourne on Friday, and a man's body was found in his submerged car at the Gippsland town of Woodside on Thursday.
SES Victoria has had more than 7400 requests for help, with about 5800 related to fallen trees.
Mr Wiebusch said as of mid-Friday afternoon, more than 100,000 homes were still without power and 100 roads remained closed, particularly through the Dandenong Ranges.
A strong wind warning was also issued on Friday for Gippsland Lakes and the eastern and central Gippsland coasts.
Those already in a safe place in Gippsland are urged to stay put for the next 24 to 48 hours when most of the flooding is expected to move through.
Authorities are pleading with locals not to drive through floodwaters.
