Ranked 108th, Hlavackova specializes in doubles. Teaming up with fellow Czech player Lucie Hradecka, she won the French Open in 2011 and finished runner-up at Wimbledon, the London Olympics and the U.S. Open last year.
"It was a very tough match to win," Hlavackova said. "Yvonne had two great weeks in a row so she was playing well. But I had a great week as well here and I don't really want to go home now."
Hlavackova was the more attacking player but struggled with her opponent's high topspin balls from the baseline.
Meusburger conceded a 4-2 lead but broke Hlavackova again for 6-5 and wrapped up the opening set with an ace.
The Austrian avoided break points in the second set and broke Hlavackova's serve twice to go 5-2 up. Meusburger clinched the title with a volley winner on her second match point.
Earlier Sunday, Austrian doubles player Sandra Klemenschits also won her first WTA title, five years after battling abdominal cancer, the same illness her twin sister and former doubles partner Daniela died of in April 2008.
Klemenschits and Andreja Klepac of Slovenia defeated Kristina Barrois of Germany and Eleni Daniilidou of Greece 6-1, 6-4.