The world number 155 was one of three players to come from a set down on Thursday to seal a quarter-final spot in the WTA International hard-court event, beating Koukalova 6-7 (4-7) 6-4 6-0.
In a an opening set littered with double faults and breaks of serve, it was Koukalova who took an early lead after the tie-break, however she was unable to continue that momentum as Kirilenko tidied her game up.
Only 46 per cent of the Russian's first serves went in during the first set, but she slowly began to improve and by the decider it was up to 76 per cent.
Having won four successive games in the second set to level the match, the 27-year-old took the final seven to progress to a last-eight clash against Kaia Kanepi.
The sixth seed also put the loss of her first set against Kristyna Pliskova behind her as she recorded a 3-6 6-3 6-2 victory.
A tight opening set saw Pliskova convert one of her two break chances to move ahead but Kanepi fought back strongly and levelled having won 55 per cent of points in the second.
With momentum on her side, Kanepi raced into the last eight with three breaks of serve in the final set, securing her win in one hour 44 minutes.
Nicole Gibbs was the third player to come back from a shaky start in Seoul as the American put a disastrous first set behind her to win 1-6 6-4 7-6 (7-5) against Danka Kovinic.
Gibbs lost seven straight games early in the match but rallied to book her first WTA quarter-final.
Meanwhile, fourth seed Magdalena Rybarikova had no such problems in her second-round match with Yanina Wickmayer.
Rybarikova fired six aces and broke her Belgian opponent five times on her way to a comfortable 6-2 6-2 win.