After South Africa scored a massive 8(dec)-525 batting first with Hashim Amla, Faf du Plessis and Dean Elgar all scoring centuries, New Zealand slumped to 6-47 by stumps on the second day at St George's Park.
While Watling showed good fight on Sunday morning along with good support from No. 11 Trent Boult, New Zealand only managed to scramble to 121 to still be a massive 404 behind South Africa on the first innings.
Now at stumps on the third day, Watling is again playing a fighting innings remaining 41 not out with Brownlie also not out on 44 with New Zealand 4-157 and requiring a further 247 just to make the Proteas bat again.
After being bowled out for 45 in the first innings in Cape Town on the way to an innings and 27-run defeat, New Zealand's only positive out of the first two days was that at 6-47 they at least beat that 45.
Watling was terrific on the morning of the third day making 63 from 87 balls with 13 fours as Doug Bracewell (7), Neil Wagner (0) and Jeetan Patel (0) fell at the other end.
Watling then received some support from Boult, who made an unbeaten 17, with the wicket-keeper batsman the last wicket out when he was caught by Graeme Smith off Morne Morkel.
Dale Steyn picked up 5-17 from 13 overs for the Proteas giving him his 19th five-wicket haul in his 62-Test match career. Robin Peterson claimed 2-20, Rory Kleinveldt 2-53 and Morkel 1-26.
The Black Caps were forced to follow-on and at least openers Martin Guptill and Brendon McCullum put up some fight on this occasion.
They combined for a gutsy 40-run opening stand from 122 balls before captain McCullum was out for 11 from 57 deliveries when trapped in front by Peterson.
Kane Williamson's horror trip to South Africa then continued when he made just 11 before being bowled by Peterson. The Black Caps were then 3-84 when Guptill's vigil ended on 48 from 122 balls when bowled by Kleinveldt.
Kleinveldt, who was playing the Test in place of the injured Vernon Philander, then picked up Daniel Flynn the very next ball to be on a hat-trick.
He missed the hat-trick and in fact Brownlie and Watling then survived the last 27 overs to stumps to put on an unbeaten partnership of 73.
At stumps, Brownlie is not out on 44 with Watling on 41 as New Zealand desperately tries to restore some pride before returning home to host England.