WaiBOP began in some style through Maksim Manko, who lashed one into the top corner after a couple of minutes, before Roy Krishna equalised in first-half stoppage time.
Auckland were lacking cohesion for much of the match and, with chances at a premium as the game wore on, a draw looked likely until the introduction of David Browne. The 18-year-old earned a questionable penalty in the 84th minute, which Adam Dickinson converted, before scoring a fine volley in added time.
It was a cruel blow for WaiBOP, who were defensively well structured and more competitive than Waikato sides of seasons past, but Auckland again showed their tenacity to snatch a win in the dying embers of the game.
At Fred Taylor Park, Waitakere enjoyed a more straight-forward triumph, creating two chances and scoring two goals to take care of Wellington.
Scottish import Jordan Lowdon was again the difference, rounding the keeper to score the first and before exchanging passes with Richard Cardozo to set up the second. The 21-year-old, who plays on the left of a front three, impressed in last week's 3-0 win over Southern and will be one to watch as the competition progresses.
Wellington had the best of the chances, with Henry Fa'arodo guilty of squandering a couple of gilt-edged opportunities, but the defending champions were far more clinical and good value for their win.
The visitors dominated the second half and, with the talent in their squad, they showed they will be a difficult proposition to deal with when their new recruits start to gel.
On Saturday, Wanderers SC - formed by New Zealand youth players preparing for the 2015 World Cup - began life in the ASB Premiership with a meritorious 2-2 draw against Canterbury at North Harbour Stadium, while Hawkes Bay edged Southern 3-2 in Napier.
Saturday
Wanderers SC 2 Canterbury United 2
Hawkes Bay United 3 Southern United 2
Sunday
Auckland City 3 WaiBOP United 1
Waitakere United 2 Team Wellington 0
