In front of a sellout crowd of 60,113 at Optus Stadium on Saturday night, Quinn Tupeau's double strike for New Zealand shortly before halftime proved to be the difference in the contest.
Slipper was given a standing ovation when he came off in the 45th minute with the All Blacks leading 17-9 in the wet conditions.
The Wallabies closed to within six points with 14 minutes remaining following a try to Len Ikitau - Australia's only one of the match.
But NZ iced the game via the boot of flyhalf Damian McKenzie and an after-the-siren try to Goerge Bower, sealing their 11th consecutive win over Australia - a new record.
The result meant the Wallabies lost the Bledisloe Cup series 2-0, and finished with a 2-4 record in the Rugby Championship.
If Argentina upset South Africa in Twickenham on Sunday morning (AEST), the All Blacks will win the Rugby Championship title.
A South Africa victory will secure the silverware for the Springboks.
Australia's most recent win against New Zealand came back in 2020 in Brisbane, and although they threatened for periods on Saturday night, their ill discipline in key moments let them down.
Wallabies enforcer Will Skelton, who had flown in from France to feature, lasted just 15 minutes.
He won a breakdown penalty in the second minute, had it immediately reversed for shoving an opponent and then suffered a concussion.
The All Blacks capitalised on Nick Frost's fumble at the restart to score the opening try of the match in the eighth minute through winger Leroy Carter.
The Wallabies were dealt a big blow in the 13th minute when Allan Alaalatoa's try was disallowed after it was deemed flanker Tom Hooper had produced a dangerous clean-out in the lead-up.
Hooper was yellow carded for that incident, but the Wallabies outscored the All Blacks 3-0 while down a man to open up a 9-7 lead.
Australia's enterprise with ball in hand was a feature for the first 30 minutes, but a bizarre falcon turned the momentum back NZ's way.
After producing a dangerous dribble kick, All Blacks speedster Jordie Barrett put on the afterburners and then accidentally headbutted the ball forward after Wallabies winger Harry Potter fumbled the pick up.
All Blacks centre Tupaea soccered it forward with three Wallabies players hot on his heels before regathering it to touch down.
Tupaea scored his second try just three minutes later when he exposed a weak Wallabies defence by fending off two tacklers to touch down, giving the All Blacks a 17-9 lead at the break.
Wallabies inside centre Len Ikitau was handed a yellow card just five minutes into the second half for a high tackle, but the home side were again able to hold firm despite the numerical disadvantage.
Rob Valetini's high hit on Jordie Barrett gifted McKenzie a penalty in the 62nd minute, with the visitors extending the lead to 20-9.
Hopes of a comeback victory were boosted when Ikitau touched over for a try in the 66th, but another penalty to McKenzie meant NZ had a handy nine point buffer with 10 minutes to go.
There was late drama when Wallabies substitute Josh Flook was flattened after his attempted tackle on Jordie Barrett resulted in him copping a huge hit to the head.
