Canterbury opened the scoring through Mario Hoffman after 28 minutes, and things could have been worse after referee Logan Gregory awarded a penalty - but Tom Batty got a touch and the ball rebounded off Southern's crossbar.
Canterbury probably shaded Southern in that first half, but an invigorated Southern side improved out of sight in the second half, playing a possession game that might have earned a greater winning margin.
Basil Arthur Park earned no prizes for its corrugated surface.
In fact, it helped eliminate Southern's Ross Howard in the warm-up, and Nick Hindson, limping after a tough tackle, tried to play on, but rolled his ankle on the surface.
Another casualty was former All Whites midfielder Aaron Clapham, who showed his class before he injured a shoulder early in the second half.
Southern started without Tom Jackson, Tim McLennan, Alistair Rickerby, George Milne and Ben Fitzpatrick, so coach Mike Fridge still has many options up his sleeve.
Both keepers, Batty and Liam Little, got a half each, Matt Joy was steady as usual in central defence, where he was partnered by Cam Attwood, and Andrew Ridden, David Hayman and Craig Ferguson also featured.
A swarming midfield featured Eder Franchini and Victor Da Costa, who competed well, and both Tom Connor and Morgan Day put in good shifts.
Southern's fitness levels looked good, and there were some effective and incisive passing movements that finished in the penalty box, where big Josh Stewart and later Taylor McCormack caused Canterbury problems.
Da Costa converted a penalty for Southern, and just when all the soaked spectators were starting to head home, McCormack finished off an 85th minute cross, and a morale-boosting win was clinched Southern now looks forward to its opening ASB Premiership game against Auckland at Forsyth Barr Stadium this Saturday.
At Tahuna Park yesterday, Southern's unbeaten youth side edged out Wellington 2-1 in a national league game.
Southern youth again started slowly and it took a couple of top saves by Josh Dijkstra to deny Wellington.
However, in perfect conditions, coach Kevin Scoullar's side built from a steady platform at the back, well led by Tyrrell Barringer-Tahiri, and exerted enough pressure to have scored a couple by halftime.
The breakthrough came in the second half, when Wellington's keeper and defenders contrived to pass the ball to Lewis Jackson in front of an empty goal mouth, and Southern went ahead in the 51st minute.
Eight minutes later, Jackson did it again, scoring from a close-range header, to take his tally to four goals in two matches.
Wellington charged back into the game with an 85th minute goal by former Queenstown player Finn Moore, and as the capital side poured forward looking for an equaliser, there were a few committed tackles from Southern to preserve its win.
''The lads showed mental and physical toughness throughout the game, and it proved that a 2-0 scoreline is the most dangerous in football,'' Scoullar said.
In a national women's league game yesterday, a weakened Football South side was beaten 3-1 by Auckland City.
