Auckland is said to have received 75% of its usual summer rainfall in just 15 hours.
A local state of emergency was declared as authorities managed evacuations and widespread flooding.
New Zealand's Prime Minister Chris Hipkins thanked emergency services for their swift response to the disaster.
The new prime minister travelled to Auckland, where he also expressed his condolences to the loved ones of those who died in the floods.
"The loss of life underscores the sheer scale of this weather event and how quickly it turned tragic", he said in a news conference on Saturday afternoon.
The downpour flooded the airport, shifted houses and resulted in power cuts to homes for hours.
New Zealand's defence forces were mobilised to assist with evacuations and emergency shelters were set up across the city.
Ricardo Menendez March, a Green MP and Auckland resident, told the BBC that the area he lived in was quickly flooded and he had to evacuate, but was given shelter by a friend nearby.
"There were people who were unfortunately not as lucky - low-income communities, disabled people, migrant communities as well," he said.
Footage online showed people trapped in waist-deep floodwater and rescuers carrying out evacuations on kayaks. Other pictures showed grocery items floating down the aisles of several flooded supermarkets.
International departures were grounded from Auckland airport until at least 05:00 local time on Sunday, with no international arrivals before 07:00.
Auckland Emergency Management (AEM) said they had shifted their focus from evacuations to the clean-up effort after the rain.
They reminded locals not to travel unless it was necessary and said in a tweet to "not let today's 'less rain' trick you into planning a weekend day out".
More severe weather is forecast across Auckland until Tuesday, according to the MetService.
The National Institute of Water and Atmospheric Research (NIWA), the country's climate science body, said Friday was the wettest day on record for a number of locations in Auckland. Heavy rains were forecast in various parts of the city for at least the next five days.
"It goes without saying that we need to have a conversation about how climate change is making these events more frequent and how cities like Auckland are massively underprepared," said Mr March.
While climate scientists have cautioned against attributing individual weather events to climate change, research by NIWA has found the warming planet is leading to more extreme weather in New Zealand.