APIA became champions for the first time since the competition started seven years ago with a 2-1 victory over their old rivals thanks to a winning goal from captain Sean Symons in extra time.
Paul Galimi had given APIA a first-half lead before Matt Bilic equalised for United just before the hour mark.
Yet the euphoria surrounding APIA's triumph was mixed with disappointment because their gallant effort in a superb contest that would not have felt out of place in the A-League will not be rewarded with a tilt at the seventh Australian NPL finals that kick off on September 21-22.
The reason is because Wollongong Wolves, having won the premiership, earned the right to represent the NSW federation in the eight-team national finals. This is just not right.
It has nothing to do with the age-old controversy surrounding the merits or otherwise of winning the premiership or the championship.
It is all about Football Federation Australia's obligation to encourage consistency, especially since it considers the winners of the A-League grand final and not the winners of the Premiers' Plate as the national champions.
If the winners of any of the NPL grand finals around Australia (except Tasmania which does not have a finals series) are considered the champions of each respective federation, then it should be them who should play in the national finals not the premiers.
If, on the other hand, FFA is happy for the premiers to be rewarded with a spot in the national finals it should ask the federations to declare them and not the grand final winners as champions.
"I'm obviously delighted with the win but disappointed we cannot progress any further," APIA chairman Jim Apostolovski said later. "As champions of NSW we should be the team to represent our federation in the national finals."
FFA should exert its influence to fix this glaring discrepancy by either making the grand final more meaningful by giving the winners a spot in the finals or by rewarding the team finishing first past the post with the championship.
A point worth remembering, too, is the team that wins the Australian championship gains automatic entry to the last 32 of the following FFA Cup so APIA as new champions are denied this opportunity.
You could tell by just looking at the faces of the players and their supporters how much victory meant to APIA, who had lost the previous two grand finals.
Yet the fact that APIA won't test themselves at the next level in the national finals as a natural progression from winning the league made their triumph a bit of an anti-climax.
The FFA, as the body responsible for the NPL, has given the A-League the autonomy the professional clubs have sought for years but the game's governing body will hang on to the NPL even when a second division comes to fruition.
The ownership structure of a second-tier competition has yet to be determined but it is likely to be an asset that is wholly or majority-owned by the FFA so the NPL will be under the control of head office for the foreseeable future.
The FFA admittedly has other more important issues to deal with at the moment - not least the negotiations for the next television deal that seem to be going nowhere - but it could do much worse than have a look at the NPL rules so the grand final is given the importance it deserves.
And should head office believe that winning the premiership carries more weight it should say so and encourage the federations to declare the premiers as state champions.
It'a pretty straight-forward, really.
AUSTRALIAN NPL FINAL SERIES
Match 1: Lions FC v Campbelltown City
Match 2: Maitland v Devenport
Match 3: Wollongong Wolves v Canberra Olympic
Match 4: Heidelberg Utd v Perth SC
Winner 1 v Winner 2
Winner 3 v Winner 4