The thunderstorms dumped up to 40mm of rain in some places, but were fairly mild compared to recent downpours which caused widespread flash flooding.
About a dozen homes in Tatura, near Shepparton, were damaged, with the roof blown off one property, State Emergency Service (SES) media manager Lachlan Quick said.
The SES received 30 requests for help from residents in the south-western suburbs of Newport and Altona at the height of the storm at 9-10pm (AEDT) on Thursday.
"One was for lightning striking a roof and blowing a bit of a hole in it," Mr Quick said.
The thunderstorm was mainly confined to Melbourne and the north and northeast of the state on Thursday night and into the early hours of Friday.
Shepparton copped 42mm of rain, Tatura 41mm and Yarrawonga 29mm, while in Melbourne the highest rainfall was in the outer south-eastern suburb of Cranbourne with 20mm.
Bureau of Meteorology senior forecaster Richard Carlyon said there were two sharp bursts of rain in the state's north, but it was nothing compared to last Friday's storm and January's rains.
"If this was a regular summer we'd be saying this was a real dump of rain we've had over the last 24 hours, but now when we were having three figures in short periods of time - 100mm like last Friday and also like January - it looks more meagre," Mr Carlyon said.
On Thursday night authorities closed the Princes Freeway south of Morwell, about 150km east of Melbourne, after heavy rain sparked fears of a landslip close to the nearby Hazelwood coal mine.
Victorian Energy and Resources Minister Michael O'Brien said experts had examined the situation but the precise extent of the land movement would not be known for some time.
Mr Carlyon said the forecast was for another 10-25mm of rain across the state on Friday, and possibly 50mm over the eastern ranges, before the rain clears on Saturday morning.
"We'll have a lengthy period of mostly dry weather until the middle of next week," he said.
Mr Quick said the SES was still advising residents to be aware of the conditions and to secure loose objects around properties.
He said people should also clear their gutters if possible but only if it was safe to do so.
One man died and a number of other people had to be treated by paramedics after falling from roofs and ladders after last weekend's deluge.
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