The military was called in to help as some towns experienced three times their average monthly rainfall in just two days, topping 250 millimetres (10 inches) near Dunedin.
Rivers burst their banks and landslides closed major roads, with icy conditions creating treacherous conditions for clean-up crews.
A state of emergency was in force for both Christchurch and Dunedin, with people in affected areas advised to avoid non-essential travel.
"We don't need rubberneckers... it's not going to help anybody and it's just going to upset people," Dunedin mayor David Cull said.
Around 200 homes were evacuated around Dunedin, with Cull saying it would be days before some residents could return home.
In Christchurch, authorities warned more flooding was possible at high tide late Sunday afternoon.
The New Zealand Defence Force deployed about 140 troops to help relief efforts, sandbagging vulnerable areas and using trucks to reach stranded motorists.
The official MetService forecasting bureau said more severe weather was set to lash the South Island this week, with heavy rains on the west coast from Monday.
It said flood-stricken regions would be hit again later in the week.
"All eyes will be on the forecasts for Thursday, when another cold southerly rain event looks likely to affect Canterbury and much of the South Island," it said.
