For a spell, Kennedy's tempo wavered as the wind changed direction in the last round. He had started with a three-shot lead but mixed three bogeys with a birdie in a rocky outward half.
The Queenslander steadied to par the entire back nine but could not find a birdie to reactivate his lead.
He needed help as former winner Craig Parry and Josh Geary surged past him. They looked to be duelling for the title and $94,615 prize until they made a mess of the last.
Both went into the lake on the left, Geary from the tee, Parry with his second. Geary bogeyed and fell out of a tie with Parry who double-bogeyed.
Kennedy was back in the title hunt once more and did not falter.
A year ago, he won the West Australian Open and has been working the Japanese circuit since then and felt his game was improving.
He also felt at ease at Clearwater, a course he had played a number of times in his career.
"I have never won wire to wire before, usually I come from behind," he said. "My last two years by far have been my best in professional golf."
Seasoned professional Parry would have been stunned by his last hole blunder after carving the previous 17 holes out in five under par.
He pulled his second into the lake and missed a bogey putt, failing to claim another title to go with the 2002 event when he beat a field at Paraparaumu including Tiger Woods.
Leading New Zealander Josh Geary accepted his third place finish without any rancour as he felt he had played poorly for the final two rounds.
"I would have been surprised to get into a playoff," he said.
Geary had one unplayable shot and several other shots found water rather than land, although his sharp short game allowed him to sign for a par round.
"On the range I was hitting it good but on the course under pressure I was not, I did not feel comfortable," he said.
"I am gutted but realistic. What's done is done."
Geary was joined in the top 10 by the only other Kiwi, former champion Mahal Pearce.
