Sudden and heavy rain deluged areas of Melbourne in minutes on Thursday, with homes damaged, flights delayed and traffic diverted.
The SES received more than 1500 calls for assistance, mostly for flooding and roof damage.
Showers and thunderstorms were set to continue for the state, but by Friday, conditions will have eased, the Bureau of Meteorolgy says.
"It will clear through overnight so by daybreak it should have cleared to the east and it should be a dry day," senior forecaster Dean Stewart told AAP.
WATCH: Emergency warnings
The storm did bring with it some relief to the humid and hot conditions plaguing Melbourne for days, with the temperature dropping 10C in an hour after a top of 33C.
After a minimum of 20C, Friday's forecast will be 28, partly cloudy but mostly dry for the day.
Melbourne mops up
Hundreds of residents in Melbourne have begun mopping up after violent storms brought heavy downpours and flash flooding.
The rain came quickly, with about 18mm falling in some parts in just 10 minutes on Thursday afternoon.
Residents in Elwood barely had time to react when levels at the Elwood Canal sharply rose at 3pm.
"You just couldn't get towels down quick enough," one homeowner told Nine News.
He said at the worst of it his house was inundated by water reaching up to 10cm, covering the floorboards.
Neighbours arrived just as quickly as the water to help the man sweep up.
There was some ceiling damage at The Alfred hospital after a pipe burst, affecting the recovery area adjacent to the main surgical suite.
But no patients or staff were affected and the surgery was relocated to another surgical suite, a spokesman for the hospital said.
A severe weather warning for heavy rain and thunderstorms is still current for Melbourne as the low pressure trough moves across the state slowly.
The SES has been working hard to attend more than 1500 calls for assistance since midnight.
Most of the calls have been for flooding and roof damage while a number of people had to be rescued from their cars.
"There's been people driving through floodwaters, so we're just reminding people not to do that," a spokeswoman for the SES said.
"So obviously be careful overnight because (flooding) may lead to debris and other rocks on the road that can be troublesome as well."
The downpour affected public transport, with a number of trams having to divert past flooded roads, while some trainlines experienced delays.
At Melbourne Airport flights were delayed when ground crews were called inside just before 3pm as lightning passed overhead, an airport spokesman said.
They returned to their posts about an hour and a half later, but as the forecast remained unpredictable, travellers were being urged to check with their airline for further delays.
Since 9am, Melbourne Airport had received 56.4mm of rain.
Power was also affected, with about 2500 homes and business across the state without power at 9.30pm.
The storm did bring with it some relief to the humid and hot conditions plaguing Melbourne for days, with the temperature dropping 10C in an hour after a top of 33C
It follows one of the hottest nights on record for Melbourne.
It dropped down to just 27C at 12.37am on Thursday, just short of the record 27.4C for December set in 2012.
