The storm cell, which hit Rosedale on the North Shore just after 8am, caused an hour of chaos as roads turned to rivers and spilled into business and homes.
Two motorists needed rescuing from their vehicles after they became submerged in the waist-deep floodwater.
A section of Carribean Drive was closed and lanes on the Upper Harbour Highway were blocked by the quickly rising floodwaters.
Niwa said an incredible 62.4mm of rain fell between 8am and 9am - the wettest hour in at least eight years - as the slow-moving storm cell delivered a deluge over the northern suburb.
Fire and Emergency northern shift communications manager Scott Osmond said firefighters rescued people from two cars that got trapped in floodwaters on Rosedale Rd and Caribbean Drive.
About 14 homes were affected by flooding and firefighters cleared blocked drains to help the water drain away.
Floodwaters started to abate about an hour after the deluge began, but MetService warned it as just a foretaste of things to come today.
Forecaster Tom Adams said much of the North Island remained under a thunderstorm watch until at least 8pm.
He said similar super-sized downpours on localised areas were likely as there was little wind to move the storms away.
"There's not a lot of wind around so when a thunderstorm forms they will stay on one spot. The bad news is that there will be large amounts of rain over one spot."
He warned there was a risk of severe thunderstorms for the rest of the day.
"There are no other cells over the Auckland region but there's lots of opportunity for another two, three or four storms to pop up," said Adams.
One of those rescued this morning was Appar Singh, who was driving along Caribbean Dr when he suddenly hit the floodwaters.
His car became submerged and stopped.
"I tried to turn it on but it wasn't turning on," he said.
Singh was worried about the rising water level and called for help.
"My girlfriend was a bit scared but I tried to be brave," he said.
When Singh got out of the car the water was up to his waist.
Police said when they arrived some cars were up to their headlights in water.
North Shore resident Tamara Thompson said her trip from Hobsonville to Beachlands was interrupted by the flooding.
She came across a huge pool of water on Upper Harbour Highway, then even deeper floodwaters on Carribean Drive.
"Carribean Drive was hugely flooded. No one could get past really - but some cars were still trying."
She described pandemonium as traffic backed up and people did U-turns to avoid floodwater.
The floodwaters started to subside soon after the rain stopped and roads and highways reopened. Stranded vehicles were cleared by tow trucks.
