Debutant flyhalf Tom Taylor put on an assured display with 14 points and a composed performance in general play, while Israel Dagg added a penalty when his Crusaders team mate was receiving medical treatment for a rib injury late in the game.
"He was outstanding considering the circumstances that he is in to come into the team," All Blacks coach Steve Hansen told reporters of Taylor's impressive debut after injury ruled out Daniel Carter, Aaron Cruden and Beauden Barrett.
"Everyone knows he's the fourth choice, he comes with a lot of pressure because he is the son of an All Black (Warwick Taylor). I thought he coped tremendously well all week."
Christian Leali'ifano kicked three penalties for the Wallabies and converted Israel Folau's late intercept try but the script followed a regular pattern for the visitors, who have not beaten the All Blacks in New Zealand since 2001.
The All Blacks have held the Bledisloe Cup, the symbol of trans-Tasman supremacy since 2003, and the third match in the series in Dunedin on Oct. 19, which is not part of the Rugby Championship, is now a dead rubber.
The first half was reminiscent of the tournament opener in Sydney with the Wallabies making much of the early play, though unlike last week, Australia retained possession better inside the All Blacks half with scrumhalf Will Genia kicking more.
The world champions, however, again soaked up the pressure and the Wallabies were only able to convert their dominance into two Leali'ifano penalties.
"We didn't get the points on the board that I thought we deserved for different reasons," Australia coach Ewen McKenzie said. "We got six points and should have got more. We let them off the hook just before halftime."
New Zealand scored 15 points in that period just before the break after soaking up intense Wallabies pressure for the first 30 minutes, with Smith grabbing both tries before the break after some superb counter attacks.
Taylor slotted his first test points by converting the opening try and added a penalty to give the All Blacks a 10-6 lead before Steven Luatua set up another attacking opportunity, with Smith finishing off in the corner to secure a nine-point lead at the break.
"For long periods of the game they (Australia) won the moments," Hansen said. "I was very proud of our team with the way they fought back and in the end got on top."
The All Blacks forwards took over in the second half and put the Wallabies under immense pressure, particularly at the scrum, as Taylor slotted three more penalties to pad the advantage while Leali'ifano responded with his third successful kick.
Folau scored a consolation try from an intercepted pass deep inside his own half with less than 10 minutes remaining but it was not enough to spark a remarkable turnaround and Dagg completed the scoring with a routine penalty from close range.
New Zealand's next Rugby Championship match is against Argentina in Hamilton while the Wallabies host South Africa in Brisbane. Both games are on Sept. 7.