They produced a performance full of grit, combined with some superbly taken goals, to inflict Auckland City's first defeat in more than 400 days.
Jackson was the hero for Team Wellington, with two goals including a wonder strike for their first goal.
Auckland City were off their game all night, especially on attack, and their defence struggled to deal with Team Wellington's set piece threat. But they will rue several missed opportunities and the concession of a late, late penalty in the second half.
The match was an absorbing contest, befitting of a final. Auckland City looked odds-on to win the game in normal time, before a 88th minute penalty to Team Wellington, coolly converted by Cole Peverley.
Earlier Daewook Kim was set to be the hero for Auckland City, breaking a 1-1 deadlock in the 81st minute with a well placed header. But Team Wellington never stopped pushing and were rewarded when Takuya Iwata brought Ben Harris down in the penalty area, though the combative Harris was perhaps lucky to still be on the field after two crude fouls.
The early flashpoint of the match came in the 59th minute, when referee Matt Conger awarded a controversial spot kick to Auckland City
It looked an extremely harsh call, as the ball cannoned into Chris Bale's arm from his teammates' clearance near the byline. Joao Moreira duly converted, while the Wellington protests continued.
Earlier Team Wellington had taken the lead through a fabulous strike by Jackson. After dispossessing Emiliano Tade, Jackson produced a searing shot from 25 yards that rocketed past Diego Rivas in the Auckland City goal.
It was perhaps a little tough on Auckland City that the domestic season came down to 90 minutes yesterday. Ramon Tribulietx's team has been almost peerless this campaign, finishing eight points ahead of the second placed team.
Before last night, their unbeaten run in the ASB Premiership stretched across 28 matches and 421 days, going back to their last defeat in New Zealand in January 2015.
But that is the system and Team Wellington, more than any other team, deserved the chance to upset the status quo. They took their North Island rivals to penalties in the OFC Champions League final last year and the two league games this year were a 2-2 draw and a narrow 1-0 win to Auckland City.
Team Wellington 4 (T Jackson 52, C Peverley 88 pen, B Harris 93, T Jackson 99)
Auckland City 2 (J Moreira 59 pen, D Kim 81)
Halftime: 0-0
