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 either Robin Soderling or Rainer Schuettler on Saturday. Nieminen will face top-seeded David Nalbandian or Albert Montanes in the other semifinal match.
The last two quarterfinals were scheduled for the evening session.
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 quarterfinal 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 early this year to become the first Japanese singles winner on the tour since 1992.
Roger Federer withdrew from the tournament last week, leaving seventh-ranked Nalbandian as the top-seeded player.
Defending champion Ivo Karlovic skipped the tournament, held for the 40th time.
Pablo Remaining Positive
Nishikori, Ancic advance in Stockholm
