The preschooler, identified as Ayan Kapoor, died after being struck by a tree on Hawthorn Rd in Melbourne's Blackburn South on Thursday evening.

A family member told Nine News that Ayan had only been outside for a couple of minutes before he was struck and then rushed to hospital where he later died.

A 36-year-old woman was also killed after a tree hit the ute in which she was a passenger at Fernshaw, in regional Victoria, about 7pm.

The 24-year-old male driver was taken to hospital with minor injuries.

In another incident, a 59-year-old man died after a tree fell on his car as he was leaving a shopping centre in the Melbourne suburb of Belgrave.

The early-evening storm caused widespread power outages and water contamination concerns, with Melbourne residents told to boil drinking water.

"The risk is not huge," chief health officer Brett Sutton said.

"I wouldn't say people should be really concerned. I don't expect a spike in gastro."

Supplier Yarra Water said an outage at the Silvan Reservoir, 40km east of Melbourne, meant untreated water was released into the system.

That affects about 250,000 homes in 88 suburbs mainly across the city's north and east.

On Friday afternoon, Yarra Water said it was working to flush the system and would confirm when the boiled water advisory was withdrawn.

Premier Daniel Andrews offered his condolences to the families of those killed.

Mr Andrew noted it was "no ordinary storm event", occurring against the backdrop of strict COVID-19 rules for metropolitan Melbourne and regional Victoria.

To help people to legally render assistance, Victoria's Department of Health and Human Services has issued detailed advice online as the clean-up could take days

"That is not an invitation for people to do things that don't need to be done," the premier told reporters on Friday.

"But we do recognise ... there will be other needs that will need to be met by perhaps a family member."

Under the updated advice, residents whose homes have been damaged by the storm are allowed to leave home to buy materials to fix their house, have tradespeople come into their home, seek alternative accommodation and look for lost pets.

As of Friday morning, Victoria's State Emergency Service had logged more than 2000 calls for help, with most for downed trees and about 10 per cent building damage-related.

The worst-hit areas were Mount Evelyn, Belgrave, Croydon, Lilydale and Mount Waverley - all in Melbourne's east.

A wind gust of 158km/h was recorded at Wilsons Promontory, about 200km from Melbourne, during Thursday's weather event.

In the city, the strongest gusts were felt at the Fawkner Beacon (115km/h), St Kilda Harbour (111km/h) and Avalon (104km/h).

AusNet, power supplier to the state's east, said 121,000 customers had been impacted across its network.

Some 52,458 customers awoke without power but outages had dropped below 27,000 by 4pm.

"Some customers will be back on today but for some of them it could take days," an AusNet spokeswoman told AAP.

A further 40,000 customers of United Energy, the energy provider to Melbourne's inner southeast and Mornington Peninsula, had their power go offline at the peak of Thursday's storm.

At 4pm, less than 2000 outages were yet to be rectified.

People are advised to steer clear of downed powerlines and assume they're live before reporting the damage to their local energy provider.

Strong winds are forecast to hit Victoria again on Sunday.

Meteorologist Chris Arvier said gusts could reach similar levels to those that battered the state on Thursday and trigger another severe weather warning.

Australian Associated Press