The match ended tamely when he swung wildly and missed, leaving New Zealand three runs short on 162 for 7.
"We were put under pressure towards the end, some of it we put ourselves under, and we didn't respond well and that's disappointing,'' New Zealand captain Brendon McCullum said. "We talk a lot among the group that when we get ourselves in strong situations to finish games off we do it clinically and with the ruthlessness we did throughout the Zimbabwe series and the first Twenty20 game [against South Africa]. Tonight was bitterly disappointing and we are going to have to pick ourselves up pretty quickly.
"The last five overs were probably our worst five overs we have had all summer.''
They had played plenty of good cricket beforehand, restricting South Africa to 165-7 from their 20 overs, which looked about 15-20 runs short of a winning total.
Southee and Doug Bracewell had done a good job to keep them to a middling score. The pair bowled with good pace that troubled the batsmen and they weren't afraid to mix it up with short deliveries. The runs even dried up at a time when South Africa would normally look to accelerate, with one three-over stretch going for just nine runs.
They were well backed up by some fielding that was often quite brilliant at times, with Guptill pulling in a stunning left-handed catch above his head at cover to dismiss Johan Botha off Southee's bowling.
Nicol also somehow reeled in a full-blooded AB de Villiers straight drive off his own bowling to run out a dangerous JP Duminy, who had raced through to 38 off 20 deliveries.
New Zealand were quickly ahead of the asking rate, which they needed to do given the fact rain threatened all night.
Rob Nicol (33 off 19) and Martin Guptill (26 off 19) put on 65 for the first wicket in quick time and Ryder continued the momentum but a brief interruption for rain changed the complexion of the match.
The Black Caps were cruising at 131-3 after 14 overs when they scampered off but the Proteas stayed on pitch, given they were behind on the Duckworth-Lewis method, and the rain eased even before the ground staff could get to the block.
New Zealand slowed to such a state they scored only four runs off the last nine balls for the loss of three wickets.
"It's a funny, old game we play,'' South Africa captain de Villiers said. "There's no room for giving up and we didn't tonight.''
McCullum said before the match the game was a "pivotal moment'' in New Zealand's already-successful summer.
The next month will reveal just how important it is, starting with Saturday's first one-dayer in Wellington.
SCOREBOARD
South Africa innings
R Levi c Nicol b Franklin 11
H Amla c McCullum b Bracewell 33
J Morkel c Nicol b Southee 10
A de Villiers b Nicol 29
J Duminy run out (Nicol) 38
J Ontong lbw Nicol 6
J Botha c Guptill b Southee 2
W Parnell not out 22
R Peterson not out 11
Extras (lb 1, wd 2, nb 0) 3
Total (for 7 wickets, 20.0 overs) 165
Fall: 1-20 (Levi), 2-39 (Morkel), 3-59 (Amla), 4-121 (Duminy), 5-129 (De Villiers), 6-130 (Ontong), 7-137 (Botha)
Bowing: R Hira 2-0-20-0 (1w), M Bates 3-0-29-0, J Franklin 2-0-23-1, T Southee 4-0-22-2, D Bracewell 4-0-28-1 (1w), N McCullum 2-0-22-0, R Nicol 3-0-20-2
New Zealand innings
R Nicol c Levi b Morkel 33
M Guptill c Amla b Botha 26
J Ryder c Morkel b Botha 52
B McCullum c de Villiers b Peterson 18
K Williamson c Morkel b Morkel 6
J Franklin not out 9
N McCullum c de Villiers b de Lange 0
D Bracewell c Amla b de Lange 0
T Southee not out 0
Extras (lb 5, wd 12, nb 1) 18
Total (for 7 wickets, 20.0 overs) 162
Fall: 1-65 (Nicol), 2-73 (Guptill), 3-112 (McCullum), 4-142 (Williamson, 15.2) 5-158 (Ryder) 6-160 (McCullum), 7-160 (Bracewell)
Bowing: R Peterson 4-0-34-1, M de Lange 4-0-36-2 (2w, 1nb), J Morkel 1-0-13-0 (1w), M Morkel 4-0-31-2 (2w), J Botha 4-0-20-2 (2w), W Parnell 1-0-14-0, J Duminy 2-0-9-0