After coming to the crease with the Knights on 161-6, Southee quickly showed his attacking intent as he went about rescuing his side's innings.
He raced to 50 from 46 balls and the milestone did nothing to slow him, with 21 taken from one Scott Kuggeleijn over. After charging past his previous best score, Southee showed no signs of nerves in the 90s and brought up his maiden ton from just 88 balls.
He and Daryl Mitchell put on 166 for the seventh wicket - a provincial record against Wellington - before Mitchell was dismissed for 43. Southee went on unabated after the loss of his partner, eventually passing 150 to drive up his first class average of 16.
The Knights declared shortly after he was dismissed by Kuggeleijn, as if sensing the sooner Southee returned to the middle the better.
They were right, with the seamer taking just six balls to remove Wellington opener Josh Brodie. Southee struck again in his third over, before dismissing Michael Papps and Ryder in his fifth to complete a memorable day.
Elsewhere, Canterbury's English import Gareth Andrew gave Southee a run for his money in the player-of-the-day stakes at Eden Park's outer oval. After beginning day two on 126no, the No 8 batsman carried on to post his own highest score of 180no before Canterbury declared on 405-9.
The Wizards also chose to give the ball to the hot hand and Andrew rewarded that decision by taking three balls to remove Lou Vincent for a golden duck.
He soon sent Reece Young back to pavilion and, with some assistance from his fellow bowlers, Auckland were in trouble on 58-5. But half centuries from Englishman Phil Mustard (55), Gareth Hopkins (96no) and Kyle Mills (61no) pushed the Aces to 264-7 at stumps.
The day's other match, between Otago and Canterbury in Dunedin, was shortened by rain, with the hosts reaching 181-4 in their first innings.