The All Blacks racked up five tries to one in a fast-moving contest in Wellington to stretch their winning streak against the Wallabies to nine straight matches and leave them with four wins from six at the end of the Rugby Championship.
Having trailed for much of the first half, the home side took a 19-13 lead on the stroke of half-time through an audacious try by Clarke before dominating the remainder of the contest.
Joe Schmidt's Wallabies crashed to their fifth Rugby Championship defeat of a troubled campaign and remain without a win over the All Blacks on New Zealand soil since 2001.
New Zealand captain Scott Barrett was pleased his team overcame their hoodoo in the country's capital city, having failed to win any of their previous five Tests in Wellington.
"Really pleased to have reversed the curse. We didn't start too well, but I'm really pleased with how we finished," lock forward Barrett said.
"We talked about owning our effort and it showed there on our line, it was pleasing to not let them in. And I'm pleased to finish on a high in our final home game."
It was an improved finish to the match for Scott Robertson's New Zealand, who have faltered badly in the closing stages of several recent Tests, including last week's 31-28 defeat of the Wallabies that saw them retain the Bledisloe Cup.
As with the Sydney contest, both teams adopted a ball-in-hand approach, with the in-form Clarke a chief beneficiary as he took his tally to seven tries in five Tests this year
It was the last home Test for two long-serving New Zealand players, with flanker Sam Cane and scrum-half TJ Perenara both moving to Japanese clubs at the end of the year.
It was also the 100th Test for former skipper Cane, who was typically industrious and received a standing ovation from a crowd of 32,000 when he was substituted in the second half.
Wallabies 'gutted'
Beauden Barrett, who started in place of Damian McKenzie at fly-half, landed four conversions for the All Blacks while Wallabies counterpart Noah Lolesio kicked eight points, including the conversion of their lone try scored by Fraser McReight.
Australia were awarded the first six penalties of the match and dominated the opening stages before flanker McReight burrowed over.
The All Blacks improved their discipline and registered three tries before the interval, all to outside backs.
Wing Sevu Reece capitalised on a break and accurate long pass from centre Anton Lienert-Brown to score, before fullback Will Jordan danced through the defence for his 35th try in 37 Tests.
The home side turned down a simple penalty shot at goal on the stroke of half-time and their gamble paid off, with Lienert-Brown's pass sending Clarke through and untouched next to the posts.
New Zealand's forwards took the upper hand as the game wore on and the result was put beyond doubt when replacement prop Tamaiti Williams and Clarke touched down in quick succession midway through the second half.
Wallabies captain Harry Wilson was disappointed his side failed to capitalise on a strong start.
"We're obviously gutted. It's not the result we came here for and wanted," loose forward Wilson said.
"Our first 40 (minutes) was really good. We showed up and started fast, but struggled with possession in the second half.
"We had a few chances which we couldn't capitalise on and they hurt us at the end."
The Wallabies finish bottom of the four-nation Rugby Championship, with their solitary victory a one-point defeat of Argentina.
New Zealand will finish second or third, with the tournament champions to be decided when leaders South Africa host the Pumas later Saturday.