The State Emergency Service (SES) says it has not seen any significant damage from an intense storm cell that has blown through Melbourne, prompting a tornado warning.

Roads across the city were inundated with rain on Friday, disrupting traffic and causing a tram to derail at Maribyrnong.

Two people who became stranded inside their cars in inner Melbourne had to be rescued.

The SES had hundreds of calls for help from people suffering from flash flooding.

"At this stage we haven't had any significant damage reported as a result of the thunderstorms," SES state commander Tim Weibusch said.

"It's mainly to do with leaking roofs a few trees down and flash flooding."

A series of severe thunderstorm warnings issued across Victoria had all been cancelled by 10:18pm by the Bureau of Meteorology.

Rainfall totals around Melbourne hit 60 millimetres at Keilor, 56mm at Sunshine, in the western suburbs, 41mm at Burnley, 36mm at Footscray and 35mm at Mooroolbark.

The city got 29mm of rain, more precipitation in three hours than for the whole of October.

Gutters were overflowing on the top end of Collins Street. ( ABC: Alison Savage )

At Flemington, the downpour turned Oaks day into a soggy mess, and was quickly christened 'Soaked Day' for those brave enough to turn up.

Earlier, funnel clouds were spotted by an observer at Melbourne Airport and a volunteer storm spotter, sparking a tornado warning from the Bureau of Meteorology.

The clouds were spotted around the airport, Craigieburn, St Albans and Campbellfield in Melbourne's northern suburbs, about 2:30pm.

A funnel cloud is only called a tornado if it touches the ground and if it did touch down, it was very short-lived.

Senior forecaster Dean Stewart said it was "pretty uncommon" for them to be issuing a tornado warning, but they did get about a dozen reports of tornadoes every year.

"Most of them are over farming communities, don't have an impact, but we do get them," he said.

"They're not usually anywhere near as intense as some of those ones we see on television in the US, most of them are fairly weak, but nevertheless, they are tornadoes."

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There was flash flooding at Newmarket station in Flemington as the storms passed through Melbourne. ( Audience submitted: Daniel Caddaye )

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