The Australian of Irish decent celebrated St. Patrick's Day with a flawless final-round 68. He finished with a 72-hole total of 17-under-par 271.
Brad Ott of the U.S. recovered from a pair of early bogeys with five birdies over the last 12 holes. He carded a 68 - one of just six rounds in the 60s Sunday at the Clearwater Resort - to take second place at 12-under 276.
Fellow American Rich Barcelo shot 69 to finish alone in third at 11-under, while Germany's Alex Cejka turned in a 70 for fourth place at minus-nine.
O'Malley began the day one shot ahead of American Joel Kribel and two clear of Andrew McLardy of South Africa. Neither pursuer could put any heat on the leader, however, as Kribel struggled to a 76 and McLardy backed up with a 75.
They tied for fifth at 8-under 280 with Aussie Nick O'Hern, who closed with a 68.
O'Malley, 36, made headlines just under a month ago when as the last-seeded player he stunned No. 1 seed Tiger Woods in the opening round of the WGC-World Match Play Championship in California.
His victory in the Clearwater Classic, the second of two events co-sanctioned by the Buy.Com and Australasian tours, was the sixth of his career. He has won three times on the European Tour and twice previously on the Australasian circuit.
The lone player to shoot all four rounds in the 60s, O'Malley dropped only three shots all week and was bogey-free for his last 44 holes.
He tied for fourth last week at the Jacobs Creek Open Championship in Australia.
American Bryce Molder, who was tied for the lead with Kribel after each of the first two rounds this week, faltered on the weekend with rounds of 77-75 to tie for 34th at 1-under par. He was the runner-up last week.
Jacob's Creek Open winner Gavin Coles of Australia finished at even-par 288.
Australian veteran Brett Ogle, 37, announced he was quitting competitive golf after completing Sunday's final round. He shot 73-69 to make the 36-hole cut by two strokes, but plummeted to 15-over par with weekend scores of 78-83.
Ogle, a professional since 1986 with 12 victories worldwide, including PGA Tour titles at the 1993 Pebble Beach Pro-Am and 1994 Hawaiian Open, cited recurring injuries and a lack of playing enjoyment as reasons for his retirement. He said he would move into television commentating.
Full field scores from the Clearwater Classic