About 280 residents of Traralgon had been ordered to leave their homes for the second time in two days as the local creek threatened to overflow.
They have been urged to take care when doing so and check for flood damage, including having electrical and gas equipment professionally tested.
The state is facing a massive clean up which could take months.
Emergency services have had more than 8000 calls since the storm hit, and more than 58,000 homes and businesses have been left without power, which could take weeks to restore for some customers.
There are currently 11 flood warnings in place around the state, including for the Yarra and Thomson rivers..
However, the Bureau of Meteorology has said the worst of the weather has probably now passed, bringing some relief for Victorians.
Emergency services have told Nine the clean-up could take months, with fallen trees currently blocking roads and isolating communities.
There are fears the storms could have also dealt a blow to Victoria’s COVID-19 vaccine rollout, with 2000 doses potentially lost due to power cuts.
The Health Department has said a batch of AstraZeneca doses is being assessed for their viability after power was lost at a vaccination site in Lilydale.