The Bureau of Meteorology issued a red warning for "very dangerous" thunderstorms, heavy rain and flash flooding across much of Melbourne and the southern Macedon Ranges on Thursday morning.
The storms left 2800 people without electricity on the Powercor network in the state's west, and also flooded major roads and brought down traffic lights in central Melbourne.
A lightning strike set a Bundoora home set alight just after 8am.
Firefighters arrived to find the house ablaze, with the fire threatening to spread to a neighbour's home.
Three people were evacuated from the property, on Betula Avenue, and were treated by paramedics before being taken to hospital.
Meanwhile, the storms brought record rains to Mildura in the state's north, which had its highest ever daily rainfall for January with 80.2mm falling in 24 hours to 9am.
The storms brought flash flooding too, with 126 calls for help to the State Emergency Service in Mildura.
"Mildura had a pretty rough night, in terms of flooding and storm damage," Premier Daniel Andrews said on Thursday.
Other areas also had dumps of rain, with 75mm at Kyneton northwest of Melbourne and 42mm at Arthurs Creek in 24 hours.
Malmsbury Headwall recorded 56.2mm of rain in an hour, while Trentham Reservoir recorded 38.6mm in the early hours of Thursday.
The storms and humidity are being caused by the remnants of ex-tropical cyclone Tiffany which formed off the Kimberley coast earlier this week.
Meteorologist Christopher Arvier from the weather bureau has warned there's more to come, with the storms predicted to redevelop later on Thursday and last into the weekend.
"We are expecting the storms to redevelop this afternoon, particularly in the western half of Victoria, bringing the risk of severe thunderstorms leading to flash flooding, and there will also be the risk of damaging wind gusts and large hail," he said.
He said the western suburbs of Melbourne would see the brunt of the next round of storms, but they would shift further east into Friday.
The Department of Transport is warning drivers and public transport passengers to "be vigilant" as weather conditions could change quickly.
Drivers are asked to leave extra space between them and the car in front, to use headlights, and pull over if the rain becomes too heavy.