Jackson's goal bulleted in from a corner kick, giving Wellington keeper Mike O'Keeffe no chance, as the Southern striker out jumped some highly rated defenders, and put his side back in the hunt after 44 minutes.
Before the match, Jackson was second top goalscorer in the ASB Golden Boot race, with six goals, and to be a contender indicates his talent and unflagging energy, especially in a side that has been on the back foot for most of the season.
Referee Isaac Travis had earlier awarded a penalty kick to Wellington in the 34th minute, which few local supporters would have agreed with, but no matter, Jarrod Smith drilled the ball past keeper Liam Little for a 1 nil lead.
Until then, Southern had matched Wellington metre for metre, in a high energy game, pressing high, living dangerously, but earning enough ball possession to threaten coach Matt Calcott's side.
But the penalty goal settled Wellington, allowing former All Whites such as newly signed striker Paul Ifill, and former Dunedin Technical defender Tim Myers, to opt for stroking passes around, and creating wide attacks.
However, building on a composed performance from Craig Ferguson, and the powerful energy of Andrew Ridden, Southern's team shape regained its edge, and the team endeared itself to spectators with ''gung ho'' attacks that were both entertaining and incisive.
A team reshuffle was required as defender Tom Connor was injured and joined Southern's bench, which already held Matt Joy, Eder Franchini, Jude Fitzpatrick, and several youth team players.
If anything, Southern responded to the new team shape with increased energy and counterattacking moves created increasing pressure with a string of corners and as Jackson's giant throw ins flew into the Wellington goalmouth, keeper O'Keeffe had to work overtime.
Runs from deep had Ridden, Tim McLennan, George Milne, Nick Hindson, all carving through, and launching crosses and shots.
Heart stopping moments for coach Calcott were another couple of Jackson headers, a couple of close range shots that were blocked, and most cardiac of all, when Ridden climbed high and rammed a header goalwards that was cleared off the Wellington goal line.
The Wellington winner came after a spell of Southern pressure in the 55th minute.
''We failed to pick up the runners, and Michael Gwyther found space to score,'' coach Mike Fridge said.
''Its been a very difficult week, with one training session cancelled due to illness, and, of course, our team captain Da Costa vanishing back to Paris.'
''But I could not be more proud of the lads that played against Wellington.
''There were no failures, everyone worked incredibly hard, and in possession, we definitely deserved to get something from the match.''
Wellington coach Calcott commented: ''Whenever we come to Dunedin, it's difficult to get a result, so we knew it would not be easy.''
