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The eight-times world champion held a slim 6.4 second lead over Finn Hirvonen when the final stages began in Auckland on Sunday, but eased to victory by almost half a minute at the end of the seven short stages.
Norway's Petter Solberg was third in a Ford, 96 seconds behind Frenchman Loeb, who won his fifth race of the season and picked up a bonus point by finishing third in the final "power" stage of the race.
'NOT PERFECT'
Loeb said: "Its been a long weekend and my driving has not been perfect.
"We made a few mistakes in the closing power stage when we were pushing too hard but the most important thing is that we have won.
"I really had to fight hard with my team mate but to finish first and second with him is an incredible result for the team, so I'm really happy ... to leave here with a victory."
Estonia's Ott Tanak produced the only real incident of the final day's racing when he rolled his Ford on the 20th stage and was forced to retire. He had been running fifth at the time.
Loeb, who also won the New Zealand rally in 2005 and 2008, has now moved to 145 points in the overall standings. Hirvonen is second in the championship with 107 points.