He finished at 20-under, but, like the rest of the field, was blown away by a resolute Ernie Els. Kelly tied for 10th.
He now island-hops from Maui to Oahu for the Sony Open.
Kelly made his debut last year in Honolulu and turned his 200th career PGA Tour start into his first career victory.
Kelly birdied the par-5 18th to edge John Cook. Cooks downfall came in his downswing on the par-3 17th. A cell phone from the gallery went off just before Cook made contact with the ball, causing him to push his tee shot into a bunker right of the green. He made bogey and finished a shot back.
Kellys triumph was worth more than the $720,000 first-place prize. The victory jumped him from 82nd to 49th in the Official World Golf Ranking, and into field in the Accenture Match Play Championship ' his first appearance in a World Golf Championships event
It continued a season of firsts for Kelly. He also qualified for his first Masters, where he tied for 20th, and played in his first Tour Championship, where he finished fourth.
After going 199 events without a win, Kelly earned his second victory just 18 starts later at the Advil Western Open.
The 36-year-old from Wisconsin is one of 28 players from last weeks field of 36 who will be playing the years first full-field event. That group includes Els, Sergio Garcia, Charles Howell III, Rich Beem, Retief Goosen, Vijay Singh, 1996 winner Jim Furyk and 99 champion Jeff Sluman.
There are 144 players in the field competing for the increased purse of $4.5 million. The winner will get $810,000.
This is the 38th playing of the event, and all have been held at the 7,060-yard, par-70 Waialae Country Club.