But the All Blacks, who will host the Lions in 2017, still prevailed 27-16 to successfully defend the Bledisloe Cup in Wellington.
Ben Smith, who scored a hat-trick in last weekend's victory in Australia, grabbed two in at the Westpac Stadium, while Tom Taylor, standing in at fly-half for Aaron Cruden, Beauden Barrett and Dan Carter, kicked four penalties and a conversion before Israel Dagg added another three-pointer late on.
A strong start by the Qantas Wallabies saw them take a 6-0 lead thanks to two penalties from Christian Leali'ifano, who nervelessly levelled the Lions series at 1-1 with a late conversion in Melbourne.
But New Zealand romped back and some superb handling from Julian Savea, Dagg and back row Steven Luatua put Smith away in the right hand corner on 27 minutes.
Taylor's conversion handed the Kiwis the lead and his penalty extended it to 10-6 before a burst from Nonu enabled Dagg to put Smith over for his seventh try in his last four Tests just before half-time.
It was a lead that the world champions rarely looked like conceding and three second-half penalties from Taylor - to Leali'ifano's one in response - saw New Zealand keep Australia at arm's length.
Folau's late effort, converted by Leali'ifano, gave the visiting fans something to cheer about and trimmed the gap to eight but Dagg's penalty, with five minutes left on the clock, was effectively the final nail in the coffin for Australia, whose winless run in New Zealand now extends to 15 matches stretching back to 2001.