The Dane was a beaten finalist in the recent US Open final as Serena Williams continued her dominance in the last grand slam of the year.
Appearing for the first time since that defeat, Wozniacki was given a stern test by Jarmila Gajdosova in Tokyo on Thursday before coming from a set down to win 4-6 7-5 6-3.
Having earned a bye in the opening round, the number-two seed made a slow start, but then rediscovered her touch afterwards to progress to the last eight.
Wozniacki was particularly impressive in the final set, breaking her opponent's serve three times to go through.
Gajdosova fashioned 14 break points of her own in the match, but was only to take five as Wozniacki thwarted the Australian world number 91.
The Dane will now face Carla Suarez Navarro after the Spaniard overcame Daria Gavrilova.
Suarez Navarro struggled through an incredible opening set, taking the tie-breaker 7-5 after a remarkable eight breaks of serve left the pair locked at 6-6.
She looked much more assured in winning the second 6-3 as Gavrilova's challenge ultimately faded.
The winner of Wozniacki's clash with Gajdosova will face either Garbine Muguruza or Casey Dellacqua in the semi-finals.
Both Muguruza and Dellacqua came through their second-round contests in straight sets on Thursday, the former dumping out fourth seed Jelena Jankovic 7-6 [7/4] 6-4 and the latter overcoming Marina Erakovic 6-2, 6-4.
Dellacqua was particularly dominant; giving up just two breaks overall as she sent down an impressive five aces to just one double-fault.