Nishikori will next face second-seeded Mario Ancic, who beat Steve Darcis 7-6 (4), 6-4.
Nishikori, who has jumped 212 spots to 77th in the rankings since the beginning of the year, was bothered by a sore knee in his opening match against eighth-seeded Marcel Granollers on Monday.
"It was better than the first match, he said. "I feel it is 80 percent healed. I didn't feel much pain during the match.''
The 18-year-old Nishikori had three break points to 5-4 in the third set when Hrbaty fell behind 0-40, but the Slovakian saved them all.
In the next game, Hrbaty was only two points from the match at 30 all, but the Japanese teenager eventually held his serve.
"I just concentrated on keeping my serve,'' he said. "I'm glad that I did not go down after failing to break his serve from 0-40. The next game was difficult.''
Nishikori broke to 6-5 with a forehand winner and then held to love to wrap up the match.
"This is the first time I'm winning so constantly and it surprises me,'' Nishikori said. "Of course I haven't faced anyone from top 10, but it gives me confidence. Now I wish to advance to the semi.''
Darcis staved off two set points when trailing 15-40 and 5-6 in the opening set. Ancic won the ensuing tiebreaker when the Belgian missed a backhand passer.
Ancic broke for the first and only time in the match to lead 3-2 when Darcis missed two straight backhand shots at 30-all. Leading 5-4, the Croat held his serve to love to end the match.
Roger Federer withdrew from the tournament last week, leaving seventh-ranked David Nalbandian as the top-seeded player.
Defending champion Ivo Karlovic skipped the tournament, held for the 40th time.
Senna: We’re Still Adjusting To Del Bosque
Nishikori advances at Japan Open
Nalbandian ousts Reynolds in Stockholm
Maniche Suffers Back Injury
