The river broke its banks late on Tuesday, flooding cafes in Southbank.

The river-level Ponyfish Bar was inundated, its watery fate captured in dramatic pictures snapped by passers-by.

The low-pressure system that hammered the state on Tuesday night forced tidal water in Port Phillip Bay up against the beach — a phenomenon known as a storm surge, which is usually only seen in tropical cyclones, said Bureau of Meteorology senior forecaster Terry Ryan.

“It was a high tide - that helps. We had gale-force westerly winds across the bay and they tend to push the water to one side of the bay, so on the whole of the eastern side of the bay the water levels are higher." he said.

“This effect of a storm surge happens quite a bit when tropical cyclones come ashore."

The storm surge forced water back up the Yarra, leading to flooding, Mr Ryan said.

Only 15 to 20 milimetres of rain actually fell during the storm, pushing the river up a little, but nowhere near enough to cause the flooding by itself.

After the storm passed, the storm surge in the bay dropped off and the swollen Yarra returned to normal levels.