Smith, who had been dropped to the bench for a breach of team protocol last weekend, replaced Piri Weepu at half-time at Forsyth Barr Stadium and scooted through the defence midway through the second half for the try which broke the 8-8 deadlock.
The All Blacks scored two tries to one to record their 14th Test win but the Springboks had their opportunities, particularly in goal-kicking where Morne Steyn, Frans Steyn and Johan Goosen combined for only two of nine attempts.
South Africa missed two early opportunities, with wing Bryan Habana unable to hold an awkward pass with the line open and Frans Steyn missing a shot at goal from almost 50m on the angle.
But when the All Blacks infringed at a breakdown, Morne Steyn kicked truly from 36m to open the scoring after 18 minutes.
However, the All Blacks struck back immediately, hooker Andrew Hore making good ground and number eight Kieran Read laying on the pass to give full-back Israel Dagg a clear run to the line to make it 5-3.
Morne Steyn was to the right with a penalty from 44m and in front and the All Blacks swept back on to the attack.
Frans Steyn was just under the bar with a penalty attempt from almost 10m inside his own half, a reminder of what distance he is capable of.
The Springboks were giving as good as they received in the forward exchanges, with lock Flip van der Merwe prominent, but Morne Steyn missed his second consecutive penalty attempt.
He then missed two other attempts at goal and the Springboks had the poor return of one success out of six to help the All Blacks lead at the interval.
The All Blacks were fortunate to be ahead, though, as the Springboks had 58% territory and forced six turnovers from the All Blacks while conceding two.
Habana threatened early in the second spell but lost the ball forward in the tackle of Aaron Smith and the chance was lost.
Habana, though, gave the Springboks the lead with a brilliant individual try eight minutes into the half. He raced from a line-out 40m out, chipped and re-gathered to score in the right corner.
But Morne Steyn missed again and Aaron Cruden kicked a neat penalty three minutes later to tie the scores at 8-8 as the arm wrestle continued.
Winger Cory Jane had been safe under the high ball for the All Blacks and made another fine take as the Springboks tried to pressurise New Zealand's back three.
South Africa were kicking too much ball away and the All Blacks made them pay when Smith dummied and sidestepped through the defence from 25m out to score a gem of a try.
South Africa suffered another blow when replacement prop Dean Greyling was sin-binned as he dived indiscriminately into a ruck.
Johan Goosen took over from the out-of-sorts Morne Steyn but missed with a long-range attempt from 55m to make it one goal from eight for the Springboks.
But he was on target from 39m soon after and it was 15-11 with 11 minutes left.
Cruden's two late penalties added gloss to the final result as the hosts held on.
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