In the city centre the National Gallery of Victoria suffered flooding, while the Docklands Stadium was among those buildings damaged during the violent storm, which washed out horse races.
Bureau of Meteorology forecaster Wasyl Drosdowsky said the hail that hit in one suburban area was up to 10 centimetres (four inches) in diameter.
"(It was) tennis ball size roughly," he said. "As far as we can tell, that's close to the biggest hail we've seen in Melbourne."
As the city readied for further violent storms Sunday, once-in-a-century floods were peaking in the state of Queensland in the country's northeast, parts of which have been in drought for almost a decade.
Townships in the state's cotton-growing south were cut off by rising flood waters and in St George the Balonne River reached 13.5 metres (44 feet), its highest level since records began in 1890.
Queensland Premier Anna Bligh said the cost of the flooding would be in the hundreds of millions of dollars, as there had been major damage to highways and rail lines had been washed away.
"This is a massive water event which has smashed all the records known here in the southwest," she told reporters Sunday as she toured St George.
Melbourne was bracing itself Sunday for further storms after a mini-cyclone ripped through Australia's second largest city, bringing with it hail stones the size of tennis balls. The storm dumped heavy rain across the southern state of Victoria, and smashed into the regional capital with winds of up to 100 kilometres (62 miles) an hour, cutting power to 100,000 homes. Some 26 millimetres (one inch) of rain fell on Melbourne within an hour while other areas recorded up to 70 millimetres during the Saturday storm.