The seventh-seeded Pliskova broke Williams' serve in the third game and held serve from there to win the first set 6-4, closing with an ace.
The 26-year-old Czech player is one set from becoming just the fifth active player to beat Williams twice or more at major tournaments.
Williams is aiming for a record-tying 24th major title. She lost to Pliskova in the U.S. Open semifinals in 2016, but leads their career head-to-heads 2-1 after winning their quarterfinal match at last year's U.S. Open.
The winner of Wednesday's match will meet U.S. Open champion and fourth-seeded Naomi Osaka in the semifinals.
Naomi Osaka has reached her first semifinal at the Australian Open with a 6-4, 6-1 victory over Elina Svitolina.
Osaka used her aggressive style and big hitting to compile a 31-11 edge in winners, including eight aces.
The No. 4-seeded Osaka is the reigning U.S. Open champion. She never had been past the fourth round at Melbourne Park.
Svitolina had her neck and shoulders massaged by a trainer during a medical timeout while trailing 3-0 in the second set.
Osaka's semifinal opponent will be 23-time major champion Serena Williams or No. 7 seed Karolina Pliskova.
Osaka beat Williams for the championship at Flushing Meadows last year in a match filled with all sorts of drama involving the American star and the chair umpire.
Serena Williams and Naomi Osaka can set up a rematch of their chaotic U.S. Open final by winning quarterfinal matches at the Australian Open.
The No. 4-seeded Osaka faces No. 6 Elina Svitolina in the first quarterfinal in Rod Laver Arena on Wednesday.
That will be followed by Williams' matchup against No. 7 Karolina Pliskova.
Osaka beat Williams for the championship in New York last September in a match filled with all sorts of drama involving the American star and the chair umpire.
In Wednesday's men's quarterfinals at Melbourne Park, 2016 Wimbledon runner-up Milos Raonic faces No. 28 Lucas Pouille during the day, while 14-time major champion Novak Djokovic takes on 2014 U.S. Open finalist Kei Nishikori at night.