MetService confirmed the storm formed west of the city and then crossed over it and Otago Peninsula before moving north.
Alibi Bar, on the corner of Princes St and the lower Octagon, was flooded when water from a manhole in the footpath entered the premises.
Staff were not surprised, a staff member, who declined to be named, said.
''It's not the first time it's happened. We're pretty used to it.''
In George St, dirt and water lay in the worst-affected store, Jay Jays Ltd, and the Fire Service was called to pump water out.
Staff declined to speak to the Otago Daily Times.
Staff at neighbouring stores said it was not the first time they had been affected.
Staff at Daniels Gemtime Jewellers and Max Fashions said the water had risen up the kerbs and passing traffic, particularly buses, had forced it on to the footpaths and into stores.
Staff from all stores along that section of the street could be seen mopping out their stores.
Most stock appeared high enough to remain dry.
Max assistant manager Anna Wilson said it happened quickly and there was little they could do to stop it.
''We saw it rising on the other side and I said to the girls, 'Go and get towels', but by the time they got back, it was in here.''
Wall Street manager Regan Bennett said sandbags had been deployed at the St Andrew St entrance, but water still poured in.
Enviro Clean and Restoration was called to help dry six Wall Street premises, including a children's wear shop, a shoe shop, a music shop, the mall manager's office and a large pharmacy.
Cafe LOL owner Paul Martin, whose premises experienced only minor problems, believed more regular removal of leaves from nearby street drains could help them cope better with such downpours.
Dunedin City Council roading engineer Peter Standring said the flooding was the result of the intensity of the rain over a short period.
It was not feasible to build a pipe network able to cover just a few extreme weather events a year, he said.
The council would investigate problems at the corner of St Andrew and George Sts.
''It has highlighted some areas that need a closer look.''
Contractors were clearing leaves and drains throughout the city and monitoring slumping on Otago Peninsula roads.