The seventh seed was the only remaining top 10 player in the draw after a raft of huge shocks at SW19.
But she was comprehensively defeated by the Dutch player, who lost just three games in the opening set before taking the second on a tie-break.
The 20th seed will now await the winner of Julia Goerges's match against Donna Vekic in the quarter-finals.
Pliskova, a former world number one, had been expected to meet Serena Williams in the semi-finals.
Williams, seeded 25th at Wimbledon, now has an even clearer path to the women's showpiece.
WOMEN'S SINGLES RESULTS
No. 20 Kiki Bertens defeats No. 7 Karolina Pliskova 6-3, 7-6
No. 11 Angelique Kerber defeats Belinda Bencic 6-3, 7-6
No. 12 Jelena Ostapenko defeats Aliaksandra Sasnovich 7-6, 6-0
No. 13 Julia Gorges defeats Donna Vekic 6-3, 6-2
No. 14 Daria Kasatkina defeats Alison Van Uytvanck 6-7, 6-3, 6-2
No. 25 Serena Williams defeats Evgeniya Rodina 6-2, 6-2
Camila Giorgi defeats Ekaterina Makarova 6-3, 6-4
Dominika Cibulkova defeats Hsieh Su-wei 6-4, 6-1