Nishikori, a Japanese playing in Stockholm for the first time, advanced when second-seeded Mario Ancic withdrew because of fever.
"I'm sick, too. I've got a sore throat and cold and my knee hurts,'' Nishikori said. "But I wanted to play the match somehow. Now I've got a day to rest and I'm sure I can play tomorrow. It's the semifinals. It's big for me.''
The 18-year-old Nishikori will play Robin Soderling on Saturday. The fourth-seeded Soderling, who is the last Swede in the main draw, defeated fifth-seeded Rainer Schuettler of Germany 6-2, 7-5.
Nieminen will face top-seeded David Nalbandian in the first semifinal match. Nalbandian ousted seventh-seeded Albert Montanes 6-4, 6-1 for his third consecutive straight-set win in the tournament.
"I played very good,'' Nalbandian said. "It's going to be tough (against Nieminen). He's different. He's a lefty. But I think if I play good I have lot of chances. I'm going to play him the way I've been playing all week.''
Nalbandian broke for 5-4 in the opening set with a cross-court backhand and then comfortably served out the set.
The seventh-ranked Argentine reeled off six straight games after trailing 1-0 in the second set, winning the match when the Spaniard's lob sailed long at match point.
Nieminen, who is making his ninth straight appearance at the Royal Tennis Hall, broke the Spaniard twice in the first set.
The Finn broke again to lead 1-0 in the second, but Hernandez broke back to 4 all. Nieminen broke again in a 12-point game to lead 5-4 and then held to win the match.
"I played perfect tennis in the first set,'' said Nieminen, who reached the 2006 final and the 2007 quarterfinals in the Swedish capital.
"In the second set I felt pain in my ankle which I hurt twice in 2006. I hit a double fault and he broke to 4-4. But I managed to win the next long game and end the match in a determined way.''
Nishikori, who has jumped 212 spots to 77th in the rankings since the beginning of the year, won his first ATP title at Delray Beach, Florida, early this year to become the first Japanese singles winner on the tour since 1992.
Roger Federer withdrew from the singles tournament last week, leaving seventh-ranked Nalbandian as the top-seeded player. Defending champion Ivo Karlovic skipped the tournament.
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Nieminen, Nishikori advance to semifinals
