The 120th-ranked Jule Niemeier struggled as she saved two set points at 5-3 down in the opening set before eventually securing the last four points of the tiebreaker.
Niemeier broke Jabeur in the first game of the second set, which set up her win after leading for one hour, 35 minutes.
This is the 23-year-old Niemeier’s third victory against a top-10 player.
German qualifier Jule Niemeier upset defending champion Ons Jabeur 7-6 (4), 6-4 in Tuesday’s first round of the Berlin Open.
Jule Niemeier upsets reigning champion Ons Jabeur in Berlin in the first round, 7-6 (4), 6-4.
Other results from Berlin
Coco Gauff defeated Czech player Katerina Siniakov 6-3, 6-4 for the American teenager’s 23rd win of the year.
The fourth-seeded Gauff next faces big-hitter Ekaterina Alexandrova, who defeated fellow Russian Liudmila Samsonova 6-4, 6-3.
Top-seeded Aryna Sabalenka eased into the second round with a 6-3, 6-2 win over veteran Vera Zvonareva in another all-Russian match.
Sabalenka converted three of her nine break points without facing any from the 38-year-old Zvonareva, a Wimbledon finalist in 2010.
Sabalenka next faces Veronika Kudermetova or Zheng Qinwen.
Elina Avanesyan saved two match points and upset sixth-seeded Daria Kasatkina with a 6-2, 3-6, 7-6 (7) win for a meeting with another Russian compatriot, Anna Blinkova.