Twice previously a quarter-finalist in Melbourne, including past year, Pavlyuchenkova's victory was her 33rd over a top-10 rival - but her first against Pliskova.
The 2018 Australian Open runner-up will face either 16th seed Elise Mertens from Belgium or American Catherine Bellis.
Sixth seed Belinda Bencic followed Pliskova out of the tournament on Saturday when she was thumped 6-0 6-1 by Anett Kontaveit.
But the second seed never looked comfortable in Saturday's warmer conditions, throwing her racquet in disgust at one changeover and generally labouring about the court throughout the two-hour, 25-minute encounter.
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Semifinalist last January, when she famously toppled Serena Williams from match points and 5-1 down, today's tentative, misfiring figure was not the same imposing Ace Queen who blasted through Kristina Mladenovic and Laura Siegemund without the loss of a set. "Maybe the best what she played against me so far", Pliskova said. But let's say I was about 40 per cent today of my game, so of course then she can feel so much better if I just don't play enough what I can play'.
Pliskova felt she was making mistakes that she would not normally make. It's a marathon and I started my marathon really, really slow and maybe she sprinted right away'. "I am hungry and motivated so hopefully can achieve more".
Pavlyuchenkova, however, had five more break point opportunities than Pliskova, including six in a marathon second game of the match that lasted nearly 18 minutes. While Pliskova forced a tiebreak in each, Pavlyuchenkova held strong to take the match.
"It hasn't sunk in yet".
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"I even had goosebumps after some points", the 28-year-old Russian said.
"Honestly, I was trying to think "OK, if I take at least one or two games on her serve, it would be amazing", because she serves so good".
German Angelique Kerber, seeded 17th, defeated Camila Giorgi 6-2 6-7 (4) 6-3 to improve her head-to-head record against the Italian to 5-0.
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