Keven Mealamu and Cory Jane both pounced on Welsh errors for the only tries of the first-half, with Carter opening his account with a conversion and a penalty.
Stephen Jones fired over a drop-goal and a penalty, while Leigh Halfpenny landed a long-distance kick to ensure the game remained a contest at the break.
But Carter took his personal points total with the boot to 17 points after the break and skipped over the try line twice before replacement Richard Kahui crossed the whitewash late on.
Carisbrook is to be torn down after more than a century of rugby to make way for the new Forsyth Barr Stadium ahead of the 2011 World Cup.
And after thrashing 14-man Ireland 66-28 last week, the All Blacks were determined to ensure the ground lived up to its House of Pain nickname one last time against Wales.
However, it was the visitors, searching for their first away win against New Zealand, who started the brightest and took the lead through Jones' drop-goal and Halfpenny's penalty.
But after Wales were penalised in front of their own posts Jimmy Cowan tapped the penalty and send Mealamu over.
Wales attempted to respond but after losing the ball on the All Blacks 22 Jane raced clear to hold off Lee Byrne for the hosts' second try.
Jones fired over another penalty before the break but Welsh hopes of a fightback were extinguished soon after when Carter slotted over a second-half penalty before combining with Jane for his first try.
Tom Prydie was then denied a score by the pace of Kahui before Cater added three more points and then ran 50 metres to grab his second try -with Kahui adding the fifth and final Kiwi score.