After scraping past the halfway cut, the 48-year-old Jones got himself into contention with a barnstorming third round of nine-under 62 and backed that up with a nerveless five-under 66 on Sunday.
His four-round total of 18-under 266 was good enough for a three-shot victory over fellow Australian John Lyras, New Zealander Ben Campbell, South Korean Jaewoong Eom and Tomoya Ikemura from Japan.
"A lot of my friends have won this tournament - Matty Griffin, Brad Kennedy - plus all the legends that have come before me," Jones said.
"To have my name engraved on the trophy is going to be pretty special."
The consistent Jones has won 19 times as a professional in a long career.
Fifteen of those triumphs have been in Japan - most recently at the 2019 Token Homemate Cup - but until Sunday he had never been able to replicate that success on his home tour.
Jones had a nervous moment at the par-5 17th hole, when his second shot flirted with the out-of-bounds area to the right of the green.
But he was able to birdie that hole and par the last before being doused in champagne by 12 mates who had flown in from Australia late on Saturday to support him in the final round.
"This is just incredible," Jones told Sky Sport NZ.
"I ground my arse off those first two rounds because I didn't have my best stuff and then yesterday, that round was pretty special.
"I two-putted from about 60 feet on the last hole, holed a nice little five-footer which, at the time, I didn't think too much of.
"Without that, I wouldn't be here.
"I don't know what's happened but I've won it and I played some pretty awesome golf, for an old guy anyway.
"It's a dream come true."
Jones began the final round four shots adrift of overnight leader Shae Wools-Cobb, who made a disastrous start with a bogey and double bogey on the opening two holes.
Wools-Cobb eventually signed for a six-over 78 and slipped all the way back to a tie for 26th.
Jones' victory in the $NZ1.65 million ($A1.52 million) event saw him jump to second on the Australasian Tour Order of Merit (OOM) behind fellow Australian David Micheluzzi, who was tied for 17th at the Millbrook resort.
The OOM winner earns a guaranteed start in the British Open at Royal Liverpool in July.
