When veteran Chris Martin then quickly removed AB de Villiers for 67 and Robin Peterson after the resumption, South Africa declared, at 347 for eight holding a lead of 302.
However New Zealand's bid to at least prolong the game and regain some pride after the first day shemozzle suffered an early stumble.
Martin Guptill steered a ball from Dale Steyn to mid wicket in the opening over, completing a miserable 1, 0 match double.
Captain Brendon McCullum, fighting his natural attacking instincts, and Kane Williamson dug in and while rarely looking entirely comfortable, battled hard and almost made it to the tea break.
Williamson, who had a couple of close shaves against the persistent Vernon Philander, succumbed just before the interval, edging to medium pacer Jacques Kallis to second slip.
Then followed New Zealand's best hour of the test, by far.
Brownlie took three boundaries in the first over of the session from Philander and simply carried on with a succession of strong back foot shots.
McCullum, buoyed by Brownlie's attacking endeavour, joined in and the runs flowed at a rapid rate.
The 50 stand took 45 balls, at one point 20 coming in the space of eight balls.
The philosophy wasn't without risk.
Brownlie was dropped twice, Dean Elgar spilling a straightforward chance at gully on 23 off Steyn, then by Alviro Petersen two balls later in the following over off Philander; and McCullum, on 39, was grassed by Kallis, diving low to his right at second slip off Steyn.
That all happened in 12 balls before Brownlie resumed his assault, taking three boundaries in successive balls off tall seamer Morne Morkel, all through the backward point-cover point region.
McCullum went to his 25th test 50 off 96 balls before the left arm spin of Robin Peterson undid him, going lbw, after a vain attempt at a reprieve from the third umpire.
The stand had produced 89 in 81 balls.
Brownlie's fourth test 50, off just 44 balls, with eight fours, followed and when drinks were taken New Zealand had scored a hectic, and entertaining 96 in an hour.
Lefthander Daniel Flynn got an inside edge to a Kallis delivery after surviving 51 minutes but Watling hung in to stumps.
Brownlie took a couple of painful blows, and was reprieved by the third umpire when given out to a catch by wicketkeeper de Villiers down the legside, which clearly showed the ball flicked his shirt.
By stumps, he'd batted a minute short of three hours in his best test innings. It had been a tough afternoon but New Zealand had at least shown some welcome character.
