Australian Open quarter-finalist Jabeur came through a tight match against Pliskova, winning 6-4, 3-6, 6-3 to set up a last-eight tie against Petra Kvitova on Thursday.
Jabeur, who became the first Arab woman to reach a Grand Slam quarter-final in Melbourne, was broken when leading 4-2 in the deciding set, but hit back immediately before claiming her first win over a top-10 player since 2018.
Barty had been expecting a tough last-16 encounter against in-form Kazakh Elena Rybakina, who has reached four WTA finals already this season.
But the world number 17 withdrew from the tournament through injury.
Australia's Barty will play either Garbine Muguruza or Dayana Yastremska for a semi-final spot.
Earlier on Wednesday, two-time Wimbledon winner Kvitova had battled past former Roland Garros champion Jelena Ostapenko 6-2, 5-7, 6-1.
The Czech left-hander, 11th in the world rankings, has not lost to a player ranked outside the top 40 since last year's US Open, but said she struggled in windy conditions.
"There's no chance to have tactics in this wind," she told wtatennis.com.
"The wind changes everything. I tried to stay there, to be patient, but sometimes it's a little difficult."
Swiss fourth seed Belinda Bencic cruised past Yulia Putintseva 6-4, 6-3 and will face Svetlana Kuznetsova in the quarters after the Russian veteran was also the beneficiary of a walkover as American teenager Amanda Anisimova pulled out of the event.
Elsewhere, Belarusian ninth seed Aryna Sabalenka thrashed Maria Sakkari 6-3, 6-0 to set up a tie with China's Zheng Saisai, who knocked out seventh-seeded Dutchwoman Kiki Bertens.