Auckland now have 10 points through four games, three ahead of the only team to have taken points off them so far this season - Hawke's Bay United, who have played a game less.
In third spot are Team Wellington who compounded Waitakere's misery with a home victory at David Farrington Park.
Waitakere fired their player-coach Brian Shelley midweek following a 5-1 defeat at the hands of WaiBOP United, but new coach Chris Milicich couldn't create a quick turnaround.
Former Wellington Phoenix defender James Musa was the star, scoring a first-half header and a second-half half-volley to cancel out Nathaniel Bowen's goal for Waitakere. He then turned provider, being part of an intricate build-up to set up Joseph Dixon for the game-sealing third goal.
In today's other contest, Southern United picked up their first win of the season in the battle of the cellar dwellers. A seventh minute goal from Andrew Ridden was enough for a 1-0 win over the Wellington Phoenix Reserves, who are now the only winless side in the competition.
Earlier in the round, Hawke's Bay defeated WaiBOP 1-0.