Barty went down 3-6 6-2 6-3 in a compelling contest against Alison Riske on No. 2 Court, while Czech Republic's third seed Pliskova went down to compatriot Karolina Muchova 4-6 7-5 13-11 in an epic encounter.
French Open champion Barty had not lost for two months heading into her fourth-round match but had no complaints as Riske turned in a stirring display.
"Overall I didn't play a poor match. When I needed to, when the big moments were there, Alison played better," she said. "Tough one to swallow but I lost to a better player."
Riske is relishing her reward of a showdown with Williams, who she has partnered in Fed Cup doubles.
"I think it's super exciting. I played doubles with Serena, but never played against her. It will be an interesting match," she said.
"I'm ready for a war. She's the greatest athlete I think that's ever been on the women's side. It's going to be a huge challenge."
Riske will face Serena Williams – a 6-2 6-2 winner over Carla Suarez Navarro - in an all-American quarter but 15-year-old sensation Cori Gauff had her superb run at Wimbledon ended by Simona Halep in straight sets.
Halep is now the highest seed left in the draw after Britain's Johanna Konta kept home interest alive with a thrilling 4-6 6-2 6-4 win over world number six Petra Kvitova.