Speedster Taylor McCormack grabbed the vital 44th-minute goal, when he accelerated on to a Scott Gannon pass and beat keeper Daniel Clarke with a low, accurate shot inside the left upright.
It was no more than Otago deserved. McCormack went on to have a dynamic game frightening defenders with his pace and aggressive attitude, and not allowing Wellington to play out from the back as it normally does.
Otago coach Tony Martin was delighted with his team's first half, and the threat of McCormack, plus equally pacey Finn Moore running on to some well-constructed attacks.
The game featured steady defensive shifts from Cam Atwood, Wil MacIntyre, and Peter Overmire that protected keeper Zayne Officer, while on the break Geordie Mansford and Ross Howard launched wide attacks from deep that upset the Wellingtonians.
Howard in particular not only showed pace in attack, but also bottled up coach Stu Pine's tall striker Birthanu Taye, with safe positional play and some excellent tackling.
Keeper Officer also made a couple of critical saves, and happily watched one shot by Taye cannon off his goal upright.
If Otago dominated the first, then in the second spell Wellington's class emerged, with quality patterned football and impressive games from central midfielder Clayton Lewis, Makoii Taban and captain Daniel Bowkett. Predictably, one goal was not enough, and as Wellington pushed men forward, Otago lost confidence and started to defend too deeply.
Yet the pattern, while bad for coach Martin's nerves, also left gaps that Otago exposed with counter-attacks. Wellington's most sustained attack featured several corners that shot against the woodwork, and some last-ditch tackling and long clearances.
But, eventually, referee Ed Cook blew for fulltime and Otago celebrated.
Wellington coach Pine said his side launched too many shots astray, yet he thought the second-half effort should have yielded some reward.
Otago coach Martin pointed out that last season his team might have buckled in the second half, but yesterday they showed defensive grit, and throughout the match ''might have scored another couple and saved my nerves in the final exchanges''.
Leader Wellington has nine points, Otago now has six points, and with bottom side Manawatu to play at the weekend, a late charge up the table is not impossible.
Otago United Youth ... 1
Wellington Youth ... 0
