The second-seeded Bogomolov, a quarter-finalist here last year, rallied after dropping the first set but lost five games in only 14 minutes in the decider to bow out.
Third-seeded Mikhail Youzhny of Russia defeated Grega Zemlja of Slovenia 6-1, 6-3 to reach his third quarter-final in Zagreb.
Marcos Baghdatis, seeded sixth and the 2007 champion, downed Lukasz Kubot of Poland 6-4, 6-2.
"I kept the momentum. I feel good and hope my rankings will go up," said Baghdatis.
Results from the fourth day of the ATP Zagreb indoor tournament on Thursday (x denotes seeding):
Second round
Marcos Baghdatis (CYP x6) bt Lukasz Kubot (POL) 6-4, 6-2
Lukas Lacko (SVK) bt Alex Bogomolov Jr. (RUS x2) 6-0, 6-7 (1/7), 6-1
Mikhail Youzhny (RUS x3) bt Grega Zemlja (SLO) 6-1, 6-3
Ivan Dodig (CRO x4) bt Guillermo Garcia-Lopez (ESP) 4-6, 6-4, 6-4