The South African had four birdies and a bogey at Castello di Tolcinasco Golf and Country Club to finish at 25-under 263. Wilson, an Englishman, shot an 8-under 64, the best round of the day.
"It's great to win at last," said Otto, who failed to defend a five-shot advantage going into the final round of the Madeira Islands Open in March. "I have been working very hard on my putting and I don't think I've ever holed more long putts than I did this week."
Robert Karlsson, who shot a course-record 61 Friday, had a 5-under 67 to finish third, two shots behind.
"It was a good try, I suppose, but I haven't really played that well over the weekend and that is why I have come up a bit short," the Swede said.
Two-time major champion John Daly (67) finished 12 shots behind at 275.