Melbourne can look forward to a calm few days after the city was battered by wild winds and intense storms that caused commuter chaos on some train lines and a messy peak hour commute for some motorists.

The Bureau of Meteorology earlier today issued a weather warning as damaging winds of nearly 100km/h bashed parts of Victoria.

Winds gusts at Melbourne Airport exceeded 91km/h, while in Ballarat peaks gusts have exceed 100km/h. In Port Phillip peak wind gusts have exceeded 125km/h.

The winds knocked over this tree at a yard in Langwarrin. Picture: Deanne Wilkinson (Supplied)

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The BoM forecast for tomorrow in Melbourne has winds reaching less than half that, topping at 45km/h.

Rain is due to sweep in on Thursday and Friday before a cloudy weekend.

Wild waves blast over Mornington Pier this afternoon. Picture: Mark Spencer (Nine)

Metro Trains issued several notices on Twitter about delayed services ahead of the afternoon commuter rush.

On the Glen Waverley line, buses are replaces trains between Burnley and Darling after a tree fell onto the tracks at Glen Iris.

At least 14 buses were ordered but Metro Trains say they would take over an hour to arrive.

Residents were warned the wind gusts could bring down trees and power lines, resulting in power outages around the state.

Luckily, the storm didn't appear to cause any major power outages.

Trees came down in Malvern and Elsternwick, while in Emerald there were calls to the SES for damage.

A tree has fallen on the tracks at Glen Iris station, causing afternoon chaos on the Glen Waverley line. Picture: 9NEWS (Nine)

Damaging winds of 120km/h also hit the Alpine areas across the state.

VicRoads warned drivers ahead of the severe weather to slow down and take extra care during the afternoon rush.

Motorists were urged to be cautious of debris on the roads due to high winds.

The strong winds have knocked a tree onto a home in the Melbourne suburb of Elsternwick. Picture: 9NEWS (Nine)