World number seven Konta struggled behind her serve throughout, being broken on four occasions over a match that stretched to two hours and 26 minutes.
The Brit, playing her first match since being knocked out of the US Open by Aleksandra Krunic, raced into a three-game lead but Strycova ruthlessly served it out after securing a third and decisive break of serve in game 11 of the first stanza.
The 26-year-old again was in the ascendancy in the second but, leading 5-3, dropped her serve before passing up two break back and set points leading 5-4.
Kvitova beats Britain's Konta, Barty to face Azarenka
And Strycova, whose best showing at a Grand Slam was a last eight spot at Wimbledon in 2014, held her nerve in the tie-break to secure a quarter-final encounter against Anastasia Pavlyuchenkova.
SECOND ROUND RESULTS FROM WTA TOKYO
- Barbora Strycova (Czech Republic) beat 4-Johanna Konta (Britain) 7-5 7-6(5)
- 9-Caroline Garcia (France) beat Kurumi Nara (Japan) 6-1 6-3
WTA Adelaide International
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