Trains on the Hurstbridge and Mernda lines came to a standstill. Commuters were left stranded for an hour, waiting for replacement buses to arrive.
Services only resumed at around 8.30pm, but major delays remained throughout the network.
St Albans in the city’s west was among the suburbs hardest hit – 71 millimetres of rain was dumped over the area in an hour, with 54 millimetres falling in just 30 minutes.
Avalon received 44 millimetres in just 30 minutes, and was smacked by wind gusts of up to 110km/h at the airport about 3pm.
Before the storms arrived, Melburnians had endured thick smoke for the third day. Almost twice as many people called paramedics for help with breathing issues on Wednesday, with ambulance crews called to 167 cases.
More than 50 flights were cancelled at Melbourne Airport due to the smoke.
Wangaratta was the worst city in the world for air quality about 9.30am, according the World Air Quality Index project. Later in the morning, it dropped back to third-worst.
Childcare centres were told to keep children indoors, and all posties were handed P2 face masks to deliver parcels around Australia.
“We’ve told our people that if they’re sensitive to poor air quality, feeling unwell, or simply don’t feel safe being outdoors today, that indoor work can be provided as an alternative,” an Australia Post spokesman said.
Some swimming pools remained closed on Wednesday, including the Carnegie swim centre. The outdoor pools at Aquarena in Templestowe lower and the Monash aquatic centre were also briefly closed.
Racing Victoria cancelled meetings at Caulfield and Yarra Valley due to the smoke haze, but tennis players at the Australian Open qualifiers battled through poor air quality again.
The construction union’s Victoria and Tasmania branch said outdoor work conditions remained “dangerous and unhealthy”. The Construction Forestry Maritime Mining Energy Union (CFMMEU) advised members not to work when air quality was considered “very poor” or “hazardous”.
The storms brought reprieve from the haze, but wind conditions are expected to sweep bushfire smoke back into the city on Saturday.
The thunderstorms cleared the city smoke haze, while fire-ravaged communities in East Gippsland and north-east Victoria welcomed the rain.
But the weather bureau warned the downpour could create flash flooding and mudslides in fire-affected areas because of reduced vegetation.
Bureau of Meteorology forecaster Kevin Parkin said the fire grounds were vulnerable to erosion.
“The concern with thunderstorms is that they concentrate the rain to a very short period of time,” he said.
Mr Parkin said the rain and storm activity would move to the state’s north-east on Thursday. But he said there was a chance the trough could morph into a low-pressure system later in the week, bringing more rainfall.
There are 16 fires still burning across the state.
On Tuesday night, Tamboon and Tamboon South residents on the East Gippsland coast camped on a nearby beach to avoid a fire that was threatening homes.
“There was no loss of homes or structures, just some damage to fencing,” an Orbost Incident Control Centre spokeswoman said.
There are 1500 firefighters battling the blazes, including 130 from overseas and another 140 international personnel will arrive later in January.
Rachel is a breaking news reporter for The Age.
Tom Cowie is a journalist at The Age covering general news.
Ashleigh McMillan is a breaking news reporter at The Age. Got a story? Email me at firstname.lastname@example.org