The 26-year-old fired a seven-under 65, including four birdies in five holes followed by another two at the 15th and 16th, to overhaul Thorbjorn Olesen.
Wiesberger ended on 19-under at the Diamond Country Club in Atzenbrugg - not far from his home.
Ireland's Shane Lowry finished tied for second with Frenchman Thomas Levet two shots back.
Olesen ended up a further two shots back in fifth, one behind Sweden's Rikard Karlberg.
"It seems like it went my way, especially the last two holes," said Wiesberger, who became just the second Austrian to win the event, after Markus Brier in 2006.
"I had such a great country and such great fans backing me. I'm very proud to be following in such big footsteps (as Brier). I'm sure I'm not going to be the last home winner."