Wiesberger carded six birdies in a flawless round to finish 13 under par, three shots ahead of playing partner James Morrison, who also did not drop a shot in a closing 67.
Overnight leader Jaco van Zyl was two shots further back after a disappointing 73, but at least had the consolation of joining Morrison in claiming one of the three qualifying places on offer for the Open Championship.
Rafael Cabrera-Bello secured the remaining place at St Andrews thanks to a stunning back nine of 29 after going to the turn in 40, the Spaniard carding two eagles and two birdies to finish fifth, a shot behind two-time major winner Martin Kaymer.
Kaymer was within a shot of the lead after birdies on the first and third, but could only pick up one more shot before seeing his third to the 18th spin back into the water.
Wiesberger began the day three shots off the lead but took command of the tournament in stunning fashion with five birdies in six holes from the fourth after a one-hour delay due to the threat of lightning.
That gave him a four-shot lead and although Morrison closed to within two thanks to birdies on the 12th, 13th and 16th, Wiesberger crucially saved par from the back of the 17th green and rounded off his third European Tour title in style with a birdie on the last.
“It was a great year but a tough year for me so far,” said Wiesberger, who was no lower than sixth in his first four events of the season and lost a play-off for the Irish Open at Royal County Down in May.
“I have had a lot of success but just could not quite pull it off, so to stand here with the trophy makes it pretty sweet.”
The likes of Seve Ballesteros, Nick Faldo, Greg Norman, Bernhard Langer and Sandy Lyle are among the previous winners of the event and Wiesberger said: “I know the tradition of this great tournament and I am very proud to now have my name on this trophy as well.
“I hit a great shot down the fourth before they took us off the course, got a good shot in there and had some momentum building. I chipped in on the next and then holed a long putt and felt really comfortable out there.
“I played a great weekend with just one bogey and 66 and 65 is not a bad score on a great golf course.”
Wiesberger will now target a first major title after enjoying the experience of playing in the last group alongside eventual winner Rory McIlroy in the final round of the US PGA Championship last year.
“I love St Andrews and the Open and I love playing hard golf courses,” he added.
“I am really looking forward to the rest of the major season. I am going to be well prepared and on a high going up to Scotland.”
Morrison, who won the Spanish Open in May, was delighted with his performance after taking a two-shot lead into the final round in Munich last week, only to finish 11th after a closing 77.
“Last week was pretty hard to take but I came here, got back to business and my game is improving every day,” Morrison said. “I am doing all the right things.
“Bernd played superbly today, he won the tournament. Simple as that. He played fantastic.”