The Old Golds reclaimed the Hanan Shield and maintained a one-point lead over Wanganui at the top of the Heartland Championship table.
North Otago made hard work of a game it should have controlled. There was a lack of tactical leadership on the paddock and a seeming determination to play to the opposition's strength.
But South Canterbury made a multitude of changes to its dominant pack in the final quarter and let North Otago back into the game.
For North Otago coach Barry Matthews, it was another frustrating effort.
"It was a shocking performance; absolutely terrible," Matthews said.
"So many times we had numbers, we had overlaps, and guys got greedy and tried to do it on their own.
"After the game it was the biggest tongue-lashing I've ever given a side I've coached. Every team I've coached, I've earned the respect of the team, and that game was there for the taking.
"But on the paddock, the players just didn't do what they were supposed to do and this has happened all the way through."
North Otago's Taua Limuloa dominated the lineout, and No 8 Tevita Fifita produced an outstanding display against the odds, often having to take the ball from the base of a wayward scrum.
North Otago was unlucky to lose aggressive hooker Will Hurst at halftime.
In the backs, Hamish McKenzie was under pressure at scrum time, while Ben Patston kicked four penalties but contributed little else.
Luke Herden was the anchor in the backline and always looked dangerous. His interception deep inside the North Otago 22m with only a couple of minutes remaining and with the North Otago line wide open, sent South Canterbury back 80m.
South Canterbury dominated the forward exchanges, with No 8 Kali Latu, prop Matt Fetu and flanker Nick Strachan outstanding, while diminutive halfback Nick Annear was a superb distributor. At fullback, Jarred Trevathan was always eager to counterattack.
Patston kicked penalties in the 15th and the 30th minutes to give North Otago a 6-0 lead but South Canterbury's Scott Norton kicked two penalties in the last eight minutes of the spell to make it 6-6 at halftime.
Norton and Patston swapped penalties to make it 9-9, and in the 61st minute South Canterbury broke the deadlock when, from a scrum, Latu broke to his right and sent Annear racing 20m to score.
Patston kicked his fourth penalty, and five minutes from fulltime North Otago burst down the left flank to drive to the opposition line.
North Otago threw quickly to the lineout and Herden slowed the cover defence before putting Faaitu Tuamoheloa through the gap. The big centre put replacement winger Rowan McKenzie in for the winning try.
Wanganui moved to within a point of North Otago with a 67-10 win over West Coast in Greymouth.
Mid Canterbury holds third place, five points behind Wanganui, after a 30-27 win over Buller, which played the bulk of the game with only 14 players.
Buller and East Coast are tied in fourth place with 22 points, after East Coast beat Poverty Bay 30-29 at Tolaga Bay.
The scores:
Heartland Championship
• North Otago 17
Rowan McKenzie try; Ben Patston 4 pen
• South Canterbury 16
Nick Annear try; Scott Norton con, 3 pen
• Halftime: 6-6
- Terry O'Neill