UPDATED A ferocious storm has dumped 20 millimetres of rain in some parts of Melbourne as it passed through the city and smashed the southeast suburbs.
The Bureau of Meteorology issued a severe thunderstorm warning about lunchtime Thursday, telling people to brace for destructive winds, large hailstones and heavy rain.
Severe storm triggers flash flooding in Geelong
Watch heavy rain hit parts of Geelong, turning some streets into rivers.
The storm passed through Melbourne's CBD just before 1.30pm, pelting it with 4.2 millimetres of rain in 10 minutes, the weather bureau said.
The storm grew stronger as it travelled southeast towards St Kilda, Frankston, and Cranbourne, and the bureau detected a "very dangerous" thunderstorm near Pakenham at 1.45pm.
The bureau located other severe thunderstorms east of Lilydale and in the area east of Mount Dandenong and Gembrook, which were expected to hit Yarra Junction and the surrounding area.
The wild weather brought heavy rain to the outer suburbs, with 20 millimetres falling in Eumemmerring in just 10 minutes, bureau forecaster Rod Dixon said.
"There was another cell that was along the eastern side of the bay that produced 20 millimetres at Hampton as well, and 17 millimetres at Sandringham," he said.
There were reports of flash flooding on roads in Brighton as the storm passed through. The State Emergency Service received about 100 requests for assistance, mostly in the southeast suburbs, between 1.30pm and 3pm for flooding and building damage.
The small suburb of Chelsea, north of Frankston, was one of the hardest hit areas, with emergency services receiving 15 calls for help from that area alone, a SES spokeswoman said.
By 2.30pm there was sunshine and blue skies in the CBD and the severe weather warning for Melbourne was cancelled a short time later, with Mr Dixon saying Melbourne was in the clear for the rest of Thursday.
But a severe thunderstorm warning remains in place for the state's northeast, West Gippsland and South Gippsland districts and parts of the East Gippsland, central, north central and northern country districts.
A warning issued at 5pm said damaging winds, large hailstones and flash flooding could hit areas including Shepparton, Wodonga, Wangaratta, Traralgon, Moe and Bairnsdale over the next several hours.
Noojee, north of Warragul, was drenched with 26 millimetres of rain in just five minutes on Thursday afternoon, the weather bureau said.
Lightning strikes knocked out power on the Frankston line, and buses are replacing trains between Mordialloc and Carrum.
Buses were replacing trains between Newport and Werribee due to lightning causing signalling issues, but they have since resumed.
Whoa! Where's our view gone. It's bucketing down in St Kilda! pic.twitter.com/HofHRBotTs— PalaisTheatre (@PalaisTheatre) January 28, 2016
The wet weather is set to continue with the bureau is predicting rainfall every day until Monday.
The weather front that hit Melbourne on Wednesday. Photo: Leigh Henningham
The winds are going to ease into Thursday night but the rain will stick around as a grim drizzle, the bureau says.
Then on Friday, there will be more showers – this time focused on the evening.
Another thunderstorm is possible, probably over the south-eastern suburbs.
The Bureau of Meteorology's weather model at 5pm Thursday night. The low pressure system to the west of Tasmania is heading north.
On Saturday and Sunday, where the bureau's models are less precise, the expectation is for showers and possibly storms – although more will be known closer to the date.
The inclement weather is being caused by the interaction of two weather systems.
Victoria sits under a trough of low pressure, which is responsible for Thursday's rainfall. But lurking to our south out over the ocean is a second, more severe low. That will push north tonight, replacing the current system with its own and resulting in storms all weekend.
Making everything slightly more uncomfortable is the high (70 per cent) relative humidity in Melbourne, which is being caused by the low and is making everything feel very muggy.