Hoey began the day alongside James Elson at the top of the leaderboard but while the Englishman stumbled on the front nine, the 32-year-old Northern Irishman kept his nerve to edge ahead and close out the victory with a one-under-par 70.
Hoey told europeantour.com: “I guess I knew I had a good chance this week.
“The last two years I finished sixth both times, and I knew I was putting better and chipping better this year.”
Elson’s challenge was all-but ended on a disappointing outward nine that saw him notch three bogeys and two birdies, while Hoey picked up a shot at the par-five eighth to reach the turn at 10-under through 63 holes.
Elson was much more solid after the turn but a birdie and a bogey were not enough to haul in Hoey, who also recorded a birdie and a bogey as he eased to a 70 that gave him the victory at 10-under.
Elson was forced to settle for a share of second place, on eight-under, with fellow countryman Chris Gane who shot four birdies and three bogeys in a final-round 71.
Home hope Jose-Felipe Lima finished a further two shots back after a round of 68, sharing fourth place with Italy’s Federico Colombo and Scotland’s Lloyd Slatman on six-under.
Englishman Simon Wakefield broke the Porto Santo Golfe course record with a stunning nine-under-par 63 as he finished the tournament one-under.