A Christmas party at a Pakenham housing estate in the city's outer southeast was called off Saturday afternoon when heavy rainfall halted celebrations.
Organiser Samantha Thorpe said a little pond nearby became "like a raging river".
"It has never happened like this before."
A general severe thunderstorm warning was issued for most of the state - Central, East Gippsland, South West, North Central, West and South Gippsland, Wimmera, parts of the Mallee and Northern Country districts.
Thunderstorms lashed parts of Victoria, with up to 13mm of rain falling every five minutes in the early hours of Saturday and a severe weather warning was also in place for parts of Victoria including Shepparton, Seymour, Castlemaine, Kyneton, Ballarat and Wangaratta.
Emergency management commissioner Andrew Crisp said the bad weather was widespread: "There weren't too many parts of the state that have been spared the impact of the weather event we've seen over the past 48 hours," he said.
The Bureau of Meteorology's Kevin Parkyn said intense storms and heavy rain were expected to continue in Melbourne on Saturday afternoon and night. He said the relatively rare weather conditions could bring flash flooding.
The SES also took part in 25 rescues on Friday night - all people trapped in cars in floodwaters.
SES spokeswoman Susan Davie said it wasn't clear how those people got trapped.
"We just want to remind people to never drive through flood waters, it's hard to assess the depth of the water," she said.
In the 24 hours from 7am on Friday the SES received 693 requests for assistance across the state, with 123 of those calls from the Malvern area. Most calls were about flooding or building damage.
The whole state was likely to be hit with other thunderstorm cells over the weekend.
On Saturday afternoon the Bureau of Meteorology warned multiple storm cells were converging on Sydney and a particularly "dangerous thunderstorm" was heading towards Newcastle.
The storms were expected to cause heavy rainfall that may lead to flash flooding, with destructive winds and giant hailstones.
"It's got to do with the very humid atmosphere we've got," senior forecaster Dean Steward said.
The weather was similar to thunderstorm behaviour further north in the tropics, he said.
Heavy rain was also expected to lash Tasmania over the weekend. The BoM issued a severe weather warning for heavy rain in parts of the east and north-east of the state for Saturday and Sunday.
On Saturday senior meteorologist Rachel McInerney said there had been significant rainfall through the Bass Strait overnight and the rain ban would impact Tasmania over the next few days.
"We have a low pressure over south-eastern Australia that's bringing rain," she said.
That low pressure could bring heavy rain and localised flash-flooding. Heavy rain had already fallen in parts of the north-east overnight, with the highest 24-hour rainfall totals of 94mm at Gray, 85mm at Pyengana and 67mm at Flinders Island airport.
Saturday was also forecast to see gusty conditions across the north and east coasts with wind gusts expected to reach up to 80km/h.
Severe thunderstorms were possible for Sunday, with heavy rain and large hail. Flooding was also expected to develop over the weekend, and warnings were made for the South Esk River. A flood watch was in place for the north, north-east, north-west and Furneaux Islands.
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