Czech Pliskova produced an error-strewn display against the 31st seed, who will face either Russian Veronika Kudermetova or Estonia's Kaia Kanepi for a place in the quarter-finals.
Pliskova captured the biggest clay-clay-court title of her career by beating Johanna Konta 6-3, 6-4.
The 22-year-old Aussie quit tennis five years ago after finding the mental grind of the tour too much to bear.
Pliskova survived four match points and bounced back from 1-5 down in the third set to defeat Williams for a spot in the final four.
Osaka is bidding to become the first woman since Serena Williams in 2015 to win the US and Australian Opens back to back.
Williams' bid to claim her 24th Grand Slam title was ended by the seventh seed, who will now face Naomi Osaka in the semi-final.
Serna Williams beats Halep in an epic three-setter to set up a last eight clash with Czech eighth seed Karolina Pliskova.
Karolina Pliskova triumphed 6-3, 6-1 to set up a last eight meeting with either world number one Simona Halep or 23-time Grand Slam champion Serena Williams.
The 26-year-old Pliskova had picked up the injury at the recent WTA Finals in Singapore, and that she would be replaced by world doubles number one Barbora Krejcikova on the team.
The world number seven and eight, respectively, will team up with 31st-ranked Katerina Siniakova, the world number one in doubles, and 33rd-ranked Barbora Strycova, who is fifth in doubles.
Kvitova needed to win in straight sets to keep her campaign alive but struggled throughout to complete a disappointing first WTA Finals appearance since 2015.
Caroline Wozniacki's easy 6-2, 6-4 triumph in Singapore was sweet revenge for Pliskova, who lost to Wozniacki in the semis at last year's WTA Finals.
Six-time champion Serena Williams shook off a sluggish start to power past eighth-seeded Karolina Pliskova 6-4, 6-3 on Tuesday and into the US Open semi-finals.
Defeat for Halep means that Karolina Pliskova, at number seven, is the only women's top 10 seed to reach the fourth round.
Hsieh Su-Wei, who reached a career singles high ranking of 23 in 2013, welcomed the shake-up at the top of the sport.