Southern started without regular defenders Craig Ferguson and Andrew Ridden who were suspended due to having accrued yellow cards in previous matches, and several regular first teamers were also out injured.
Coach Mike Fridge said: ''Its not what you want when you face a strong Canterbury side, but I thought our lads gave everything they had in effort, and also played some really good football in patches.''
Southern's target was to challenge hard and upset the smooth Canterbury passing machine, and early exchanges suggested that Fridge's side could play its way into the match.
But a superb solo effort by Shawn O'Brien ruined the script as the Cantabrian winger cut in from the left and hammered a looping shot past keeper Liam Little in the Southern goal after 15 minutes.
And a one-goal cushion was enough for the red and blacks' experienced players to exert extended control, and from the Schwartz brothers Tom and Dan in defence, through a classy midfield featuring All White Aaron Clapham and former Scots professional Stu Kelly, coach Sean Devine's side carved out several good goal-scoring chances.
However, Southern did not buckle in that first half, and with Victor Da Costa and George Milne winning midfield possession, and Nick Hindson showing his exceptional pace wide on the left, it looked possible for Southern to climb back into the game.
A head injury to Da Costa and his substitution took some sting from Southern's attack, yet the second spell started with a strong header from a corner by Jude Fitzpatrick, and a couple of dangerous runs by Tom Jackson.
However, on the bounce, Canterbury manufactured a sustained passing movement that finished with the elusive Clapham finding space in Southern's penalty area, to convert a driven cross into a 2-nil lead for the visitors after 58 minutes.
Fridge then made several substitutions, bringing on the fresh legs of Alistair Rickerby, Will McIntyre and later Taylor McCormack, to prise a way through the Canterbury ranks.
As time ran out, increased Southern pressure and a succession of free kicks, corners and long throw-ins, got their reward as Jackson climbed through a crowded goal mouth to head a spectacular goal in the heath minute.
In a ragged finish, Canterbury used extended time for Youth team star striker Ryan Stanley to drill in a heath minute clincher of a goal for the 3-1 scoreline. Its coach Sean Devine was ''ultra pleased'' with his side's controlled performance.
Fridge praised his side's performance, with the qualification that, ''we should have had more shots at goal, and once again we conceded a couple of soft goals. We will have to do better next week in our away match to Waitakere.''
ASB Premiership
The scores
Southern United 1
Tom Jackson 88
Canterbury United 3
Shawn O'Brien 14', Aaron Clapham 57', Ryan Stanley 90+4
Halftime: 0-1
