Kvitova was playing Ekaterina Alexandrova in the last quarterfinal on Friday's schedule.
"I'm really sorry to withdraw from the St. Petersburg Ladies' Trophy due to illness," Kvitova said in a statement.
"I wasn't feeling well during my match yesterday and hoped I would feel better today, but unfortunately, that's not the case. I'm sorry not to play in front of the fans here in this beautiful city. I wish the tournament a great finish and hope to be back again next year."
Alexandrova will play now in her second semi final of the season against the winner of the match between Kiki Bertens and Anastasia Potapova.
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