"I had a rough year last year," Wiesberger said at the Himmerland Golf and Spa Resort. "It's been a hard couple of months and it's lovely to see it pay off."
France's Romain Langasque finished third, a further two strokes behind, while five golfers shared fourth spot.
Wiesberger let his advantage slip with a double bogey at the fourth but made amends at the 11th with an eagle and the two leaders were neck-and-neck on the back nine.
However, MacIntyre got into trouble off the tee at the 17th, allowing Wiesberger to take a two-shot lead going into the final hole.
The 33-year-old Austrian bogeyed the final hole but MacIntrye could not force a playoff, with his long-range putt for birdie lipping out to give Wiesberger victory in his 13th event since making his comeback to the Tour.
(Reporting by Rohith Nair in Bengaluru; editing by Tony Lawrence)
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