Auckland pulled one back on the stroke of halftime through Fabrizio Tavano, but were let down by some wayward finishing and became frustrated by the Phoenix's excellent, swarming defence in the second half.
Frustrations reached boiling point in the 88th minute as Auckland centreback Mario Bilen was shown a red card for a head butt while All White Tom Doyle was also given his marching orders for retaliation.
Auckland were without their Club World Cup centre back pairing of John Irving (who is currently trialling with Portsmouth FC in England) and Marko Dordevic and their midfield was often outmuscled by the excellent Alex Rufer, Matthew Ridenton and Andrew Blake.
Phoenix coach Andy Hedge said that once their three-goal lead was established, the Phoenix left the door open for an Auckland fight back but he was pleased with how his team stepped up to the challenge.
"When you go 3-0 up and you're a young player playing in front of a huge crowd, you tend to try and enjoy the game more so we took our foot off the pedal and allowed Auckland to build momentum with their possession which they do really well.
"Oli Sail made a handful of good saves but I think a special mention has to go to the right back Tam Dimairo. He was absolutely outstanding against Emiliano Tade, playing against one of the league's best players and kept him quiet for large periods and stopped a lot of the attacks going down that wing. I couldn't have asked for more from a defensive point of view in the second half."
In Sunday's other matches Waitakere United stunned league leaders Team Wellington 2-1 at Dave Farrington Park, while Southern United also lost at home to WaiBOP United 1-0.