A Parkdale woman, 36, was in the passenger seat of a ute travelling on the Maroondah Highway in Fernshaw when it was struck by a falling tree about 6.50pm.
She died at the scene. The driver, a 24-year-old Flinders man, was taken to hospital with minor injuries.
A 59-year-old Tecoma man was driving out of a shopping centre car park in Belgrave when a tree fell and crushed his car at the intersection of Terrys Avenue and Ena Road just after 6pm, Victoria Police said.
The man died later on Thursday.
Police will prepare reports for the Coroner on the deaths.
Victorian Premier Daniel Andrews offered his condolences to the families of the three people killed by falling trees.
“This will be just a terrible time for them and our hearts are with you in any support that we can provide on what is a terribly difficult time, we stand ready to do that,” Mr Andrews said.
He said there had been about 2000 calls for assistance to the SES and 1600 jobs completed.
About 85 per cent of the calls related to fallen trees and 19 per cent were due to building damage, mostly in Mount Evelyn, Belgrave and Croydon.
Belgrave man Josh O’Connell has described helping his neighbour to safety after trees came crashing down about 7pm on Thursday.
“When the wind picked up, it came out of nowhere,” Mr O’Connell said.
“We just heard a crazy commotion, it sounded almost like explosions. You couldn’t really tell where the trees were coming down, you just knew they were, everything was vibrating.
“At the start we were just running around the house like headless chooks, working out what we were going to do.”
Trees fell into the homes of both of his neighbours, he said, including an elderly woman aged in her mid-80s. Mr O’Connell and his housemate quickly went to her aid.
“I knew straight away she’d need some assistance whatever it is. Lucky I went over there when I did because the tree had crushed half the house,” Mr O’Connell said.
“Luckily she was OK but she had no idea what was going on.”
They smashed a window to access her, he said, and waited with her until first responders arrived to get her out of the Kaola Street home. The woman was uninjured, Mr O’Connell said.
“The first thing she wanted to know was if her cat was OK; luckily we found her cat.”
Mr O’Connnell’s house was not damaged but said he was “freezing” without power on Friday morning.
Residents in almost 90 suburbs across Victoria have been urged to boil water due to electrical damage caused by wild storms across Victoria on Thursday night. Tens of thousands of people have been without power after the storms took down power lines.
The strongest wind gust was 158km/h at Wilsons Promontory just after 7.30pm, the Bureau of Meteorology said.
Mount Gellibrand was also smacked by a 124km/h gust about 4.30pm, with a 122km/h gust at Yanakie at 5.30pm and 120km/h at Gabo Island just after 9pm.
The State Emergency Service received 1184 calls for help in the 12 hours to 6.30am, including 403 calls between 7.30pm and 8.30pm.
More than 1010 of the calls overnight were for trees down, mostly in Belgrave, Lilydale and Emerald, south-east of Melbourne.
The Maroondah Highway in Fernshaw remains closed through the Black Spur between Healesville and Narbethong, adding 90 minutes to the commute for essential workers.
On Friday morning, there were still traffic lights out in Melbourne, particularly in the east and outer-eastern suburbs.
“Crews are working to restore power and numerous trees are still being cleared,” a spokesman for the Department of Transport said on Friday morning.
Talkback radio callers reported trees and powerlines down from North Melbourne to Knox, while an entire roof came off a home in West Melbourne and landed on adjacent buildings, according to Fire Services Victoria.
An FSV spokeswoman said the scene was declared safe within half an hour and 16 firefighters secured the remaining sections of the house roof.
Minor flood warnings are in place for the Latrobe and Yarra rivers.
Forecaster Chris Arvier from the Bureau of Meteorology said the cold front moved east overnight.
Melbourne is expected to reach 17 degrees on Friday and 19 on Saturday, but Ms Arvier said another cold front could bring more gusty winds on Sunday.
“It does look like it could be another weather system where we’ll expect a severe weather warning again,” Mr Arvier said.
The cold front, expected to sweep through on Sunday afternoon, will keep temperatures down early next week.
with Rachael Dexter
Rachel is a city reporter for The Age.
Simone is a crime reporter for The Age. Most recently she covered breaking news for The Age, and before that for The Australian in Melbourne.