MacKinnon, from Dunedin, made it through the heats over the weekend then had to face three other boarders in the 20-minute final at Pines beach, near Gisborne.
The finalists had to ride 10 waves in that time.
As he went into the water for the final, MacKinnon, who won the title in 2001 and 2008, decided to head away from the other boarders.
"The final [there] were decent waves, not amazing, but I decided to paddle away from where everyone else was.
"It was a bit risky, as they were not breaking that often," he said.
"But when I got there they started to break and it was all go."
MacKinnon (29) fought off the challenges of Sam Peters, of Wellington, Reuben Quirk (Gisborne) and Luke Elliot, of Mt Maunganui, to win the title.
Forty boarders started the event.
MacKinnon now hopes to travel to Chile late next month to take place in the Arica Chilean Challenge, one of the biggest body boarding events in the world.
If he goes, he will be the only New Zealander at the event.
A massage therapy student at Otago Polytechnic, MacKinnon is looking for sponsorship and funding for the Chile trip.
He went to Hawaii in February, for the Turbo Pipeline Pro, and made it through to the fourth round.
If his ranking is good enough, he hopes to go back to the event, the biggest contest in body boarding, next year.
MacKinnon, who took up body boarding as a teenager, said he could surf, but always found body boarding more fun.
He did much of his training at the isolated beaches in the Catlins, where the waves suited him.
The sport was huge in South America, especially Brazil, and large crowds came to watch events, he said.
