The Bureau of Meteorology says central Victoria, including Melbourne, and the state's southwest will be inundated with heavy rain, damaging winds and large hail on Friday.
The worst of the storms are expected to begin from midday and continue throughout the afternoon.
Almost 10,000 Victorians remain without power on Friday, after storms ripped through the state on Thursday and into the evening.
There are 5695 AusNet customers, 3917 Powercor customers and 243 Jemena customers who are affected by blackouts as of 9:30am.
Geelong, Cape Otway and the Surf Coast were battered by heavy rain on Thursday evening, with a renewed warning issued on Friday morning.
"Strong storms have formed on the northern edge of a rain area in western Victoria in a very humid environment and are expected to produce heavy rainfall while moving in an easterly direction," the alert said.
"Severe thunderstorms are likely to produce heavy rainfall that may lead to flash flooding in the warning area over the next several hours. Locations which may be affected include Colac, Lake Bolac, Ballarat and Bacchus Marsh."
State Emergency Service volunteers received more that 450 calls for help in the six hours to 10:30pm on Thursday, as severe storms caused flash flooding in metropolitan Geelong.
The busiest SES units included South Barwon, Geelong and Sorrento, as homes, buildings and roads were flooded.
The storms come as disaster assistance is announced for Ballarat, East Gippsland, Moorabool and southwest Victorian residents after floods and storms on January 5.
The communities will receive financial support via the Commonwealth-State Disaster Recovery Funding.
"This financial support will provide for the immediate recovery needs for people whose homes or belongings have been impacted by the damaging winds, large hailstones and flash flooding in the central west," Federal Emergency Management Minister McKenzie said.
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