Also in the second round, third-seeded Tommy Haas of Germany overcame Latvia's Ernests Gulbis 6-4, 6-7 (3/7), 6-2 in match lasting more than 2 hours, 10 minutes to set up a last-eight clash with countryman Florian Mayer. The sixth-seeded Mayer beat Australia's Marinko Matosevic 2-6, 6-4, 6-2.
The 35-year-old Haas, a finalist in 2000, is bidding to win the title for the first time on his 10th appearance.
Daniel Brands of Germany will face Tipsarevic in the quarter-finals, after the German upset Frenchman Gael Monfils 6-3, 3-6, 6-0.
Results from the ATP Munich Open on Thursday (x denotes seeding):
Second round
Florian Mayer (GER x6) bt Marinko Matosevic (AUS) 2-6, 6-4, 6-2
Tommy Haas (GER x3) bt Ernests Gulbis (LAT) 6-4, 6-7(3/7), 6-1
Daniel Brands (GER) bt Gael Monfils (FRA) 6-3, 3-6, 6-0
Janko Tipsarevic (SRB x1) bt Grega Zemlja (SLO) 6-4, 6-2